From 6871ab48b68d5073d1939a08ac0a9c32b9460c7f Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 12:37:12 +0100 Subject: [PATCH 01/11] first commit --- LiveBedfiles/Pan5223_LogFile.md | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 LiveBedfiles/Pan5223_LogFile.md diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md new file mode 100644 index 00000000..ec67535a --- /dev/null +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -0,0 +1,5 @@ +# Pan5223 +This bedfile will be used to perform the variant filtering step of exome depth for R90. It is a remake of Pan5171; it is a known issue that mokabed mapps exon 18 of DIAPH1 incorrectly. While this issue was manually rectified in the VCP3 readcount bedfile (Pan5217), it was not corrected in Pan5171. + +Additionally, TBXA2R will be updated to use the MANE transcript NM_001060. + From eba8b7d88900227a8f3be0d7e72fe40ba29fbeef Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:41:34 +0100 Subject: [PATCH 02/11] save files --- LiveBedfiles/Pan5223_LogFile.md | 3 + .../RequestForms/Pan5223_request_form.csv | 117 ++++++++++++++++++ .../Pantranscriptfiles/Pan5223.txt | 91 ++++++++++++++ 3 files changed, 211 insertions(+) create mode 100644 LiveBedfiles/RequestForms/Pan5223_request_form.csv create mode 100644 LiveBedfiles/Transcripts/Pantranscriptfiles/Pan5223.txt diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index ec67535a..6755e8e6 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -3,3 +3,6 @@ This bedfile will be used to perform the variant filtering step of exome depth f Additionally, TBXA2R will be updated to use the MANE transcript NM_001060. +# Save transcript file and request form + + diff --git a/LiveBedfiles/RequestForms/Pan5223_request_form.csv b/LiveBedfiles/RequestForms/Pan5223_request_form.csv new file mode 100644 index 00000000..7c41b34b --- /dev/null +++ b/LiveBedfiles/RequestForms/Pan5223_request_form.csv @@ -0,0 +1,117 @@ +Instructions:,, +"Add genes symbols and/or transcripts to a panel in Moka +Add panel description to Moka +Answer following questions:",VCP3_R90, +,, +1. Pan number of bed file to be created,Pan5223, +2. Panel description/name (fill in a-c from Moka),, +2. a) Category,VCP3 Viapath, +2. b) SubCategory,R90, +2. c) Panel,VCP3 Viapath R90, +3. Is this BED file for RPKM?,ExomeDepth variant calling, +4. a) Is this BED file exclusively based on coordinates provided by a supplier ,No, +"4. b) If yes, does this need further padding?",N/A, +5. a) Should specific transcripts be used to create the bed file? (as opposed to all transcripts) Specific transcripts - see Moka,Yes - see below, +5. b) If specific transcripts are to be used have you provided multiple transcripts for the same gene? (if Yes please state),No, +6. What padding is required around the exons?,NA, +7. a) Should UTRs be included for ALL genes?,N/A, +7. b) Should UTRs be padded?,N/A, +8. a) Are UTRs required for SOME genes? ,N/A, +8. b) Please list genes/transcripts,N/A, +8. c) Should UTRs be padded?,No, +9. Any additional BED files to be included in this BED file? ,3608, +10. Are any further regions required to be added?,No, +Requested by:,Michael Yau, +Requested date:,06/07/2023, +,, +,Gene Name,Transcript +,ABCG5,NM_022436 +,ABCG8,NM_022437 +,ACTB,NM_001101 +,ACTN1,NM_001102 +,ACVRL1,NM_001077401 +,ANKRD26,NM_001256053 +,ANO6,NM_001025356 +,AP3B1,NM_003664 +,AP3D1,NM_003938 +,ARPC1B,NM_005720 +,BLOC1S3,NM_212550 +,BLOC1S6,NM_012388 +,CDC42,NM_001791 +,CHST14,NM_130468 +,COL3A1,NM_000090 +,CYCS,NM_018947 +,DIAPH1,NM_005219 +,DTNBP1,NM_032122 +,ENG,NM_001114753 +,ETV6,NM_001987 +,F10,NM_000504 +,F11,NM_000128 +,F12,NM_000505 +,F13A1,NM_000129 +,F13B,NM_001994 +,F2,NM_000506 +,F5,NM_000130 +,F7,NM_000131 +,F8,NM_000132 +,F9,NM_000133 +,FERMT3,NM_031471 +,FGA,NM_000508 +,FGB,NM_005141 +,FGG,NM_021870 +,FLI1,NM_002017 +,FLNA,NM_001456 +,FYB1,NM_001465 +,GATA1,NM_002049 +,GBA1,NM_000157 +,GFI1B,NM_004188 +,GGCX,NM_000821 +,GNE,NM_005476 +,GP1BA,NM_000173 +,GP1BB,NM_000407 +,GP6,NM_001083899 +,GP9,NM_000174 +,HPS1,NM_000195 +,HPS3,NM_032383 +,HPS4,NM_022081 +,HPS5,NM_181507 +,HPS6,NM_024747 +,IKZF5,NM_001271840 +,ITGA2B,NM_000419 +,ITGB3,NM_000212 +,KDSR,NM_002035 +,KLKB1,NM_000892 +,KNG1,NM_001102416 +,LMAN1,NM_005570 +,LYST,NM_000081 +,MCFD2,NM_139279 +,MECOM,NM_004991 +,MPIG6B,NM_138272 +,MPL,NM_005373 +,MYH9,NM_002473 +,NBEAL2,NM_015175 +,P2RY12,NM_022788 +,PLA2G4A,NM_024420 +,PLAU,NM_002658 +,PTGS1,NM_000962 +,RASGRP2,NM_153819 +,RBM8A,NM_005105 +,RUNX1,NM_001754 +,SERPINE1,NM_000602 +,SERPINF2,NM_000934 +,SLFN14,NM_001129820 +,SRC,NM_005417 +,STIM1,NM_003156 +,STXBP2,NM_006949 +,TBXA2R,NM_001060 +,TBXAS1,NM_001061 +,THBD,NM_000361 +,THPO,NM_000460 +,TNXB,NM_019105 +,TPM4,NM_003290 +,TUBB1,NM_030773 +,VIPAS39,NM_022067 +,VKORC1,NM_024006 +,VPS33B,NM_018668 +,VWF,NM_000552 +,WAS,NM_000377 diff --git a/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan5223.txt b/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan5223.txt new file mode 100644 index 00000000..eae961e9 --- /dev/null +++ b/LiveBedfiles/Transcripts/Pantranscriptfiles/Pan5223.txt @@ -0,0 +1,91 @@ +GuysAccession Symbol GuysAccessionVersion +NM_022436 ABCG5 0 +NM_022437 ABCG8 0 +NM_001101 ACTB 0 +NM_001102 ACTN1 0 +NM_001077401 ACVRL1 0 +NM_001256053 ANKRD26 0 +NM_001025356 ANO6 0 +NM_003664 AP3B1 0 +NM_003938 AP3D1 0 +NM_005720 ARPC1B 0 +NM_212550 BLOC1S3 0 +NM_012388 BLOC1S6 0 +NM_001791 CDC42 0 +NM_130468 CHST14 0 +NM_000090 COL3A1 0 +NM_018947 CYCS 0 +NM_005219 DIAPH1 0 +NM_032122 DTNBP1 0 +NM_001114753 ENG 0 +NM_001987 ETV6 0 +NM_000504 F10 0 +NM_000128 F11 0 +NM_000505 F12 0 +NM_000129 F13A1 0 +NM_001994 F13B 0 +NM_000506 F2 0 +NM_000130 F5 0 +NM_000131 F7 0 +NM_000132 F8 0 +NM_000133 F9 0 +NM_031471 FERMT3 0 +NM_000508 FGA 0 +NM_005141 FGB 0 +NM_021870 FGG 0 +NM_002017 FLI1 0 +NM_001456 FLNA 0 +NM_001465 FYB1 0 +NM_002049 GATA1 0 +NM_000157 GBA1 0 +NM_004188 GFI1B 0 +NM_000821 GGCX 0 +NM_005476 GNE 0 +NM_000173 GP1BA 0 +NM_000407 GP1BB 0 +NM_001083899 GP6 0 +NM_000174 GP9 0 +NM_000195 HPS1 0 +NM_032383 HPS3 0 +NM_022081 HPS4 0 +NM_181507 HPS5 0 +NM_024747 HPS6 0 +NM_001271840 IKZF5 0 +NM_000419 ITGA2B 0 +NM_000212 ITGB3 0 +NM_002035 KDSR 0 +NM_000892 KLKB1 0 +NM_001102416 KNG1 0 +NM_005570 LMAN1 0 +NM_000081 LYST 0 +NM_139279 MCFD2 0 +NM_004991 MECOM 0 +NM_138272 MPIG6B 0 +NM_005373 MPL 0 +NM_002473 MYH9 0 +NM_015175 NBEAL2 0 +NM_022788 P2RY12 0 +NM_024420 PLA2G4A 0 +NM_002658 PLAU 0 +NM_000962 PTGS1 0 +NM_153819 RASGRP2 0 +NM_005105 RBM8A 0 +NM_001754 RUNX1 0 +NM_000602 SERPINE1 0 +NM_000934 SERPINF2 0 +NM_001129820 SLFN14 0 +NM_005417 SRC 0 +NM_003156 STIM1 0 +NM_006949 STXBP2 0 +NM_001060 TBXA2R 0 +NM_001061 TBXAS1 0 +NM_000361 THBD 0 +NM_000460 THPO 0 +NM_019105 TNXB 0 +NM_003290 TPM4 0 +NM_030773 TUBB1 0 +NM_022067 VIPAS39 0 +NM_024006 VKORC1 0 +NM_018668 VPS33B 0 +NM_000552 VWF 0 +NM_000377 WAS 0 From 625a0c4cb4d95633c2d99a56b312aad2ff986a03 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:43:40 +0100 Subject: [PATCH 03/11] run mokabed --- LiveBedfiles/Pan5223_LogFile.md | 19 +- LiveBedfiles/Pan5223data.bed | 1287 ++++++++++++++++++++++ LiveBedfiles/Pan5223dataRefSeqFormat.txt | 91 ++ LiveBedfiles/Pan5223dataSambamba.bed | 1285 +++++++++++++++++++++ 4 files changed, 2681 insertions(+), 1 deletion(-) create mode 100644 LiveBedfiles/Pan5223data.bed create mode 100644 LiveBedfiles/Pan5223dataRefSeqFormat.txt create mode 100644 LiveBedfiles/Pan5223dataSambamba.bed diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index 6755e8e6..09a57682 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -3,6 +3,23 @@ This bedfile will be used to perform the variant filtering step of exome depth f Additionally, TBXA2R will be updated to use the MANE transcript NM_001060. -# Save transcript file and request form +## Save transcript file and request form +## Run mokabed +Time Stamp:2024-04-03 11:57:57.594913 +Command arguments executed: +RefSeq table format version generated as /home/dnanexus/out/Output_files/Pan5223dataRefSeqFormat.txt +/home/dnanexus/mokabed/LiveBedfiles/TestArea_for_bed_generation_script/OOBed7_uses_mirrored_database_.py --codingup 0 --codingdown 0 --useaccessions --transcripts /home/dnanexus/in/transcript_file/Pan5223.txt --minuschr --outputfile /home/dnanexus/out/Output_files/Pan5223data.bed --logfile /home/dnanexus/out/Output_files/Pan5223_LogFile.txt + Python version: 2.7.12 |Anaconda 4.2.0 (64-bit)| (default, Jul 2 2016, 17:42:40) +[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] + + getopt module file path: /home/dnanexus/anaconda2/lib/python2.7/getopt.py + + os module file path: /home/dnanexus/anaconda2/lib/python2.7/os.py + + pd class file path: /home/dnanexus/anaconda2/lib/python2.7/site-packages/pandas/__init__.py + + cruzdb module file path: /home/dnanexus/anaconda2/lib/python2.7/site-packages/cruzdb/__init__.py + +version as defined by git tag = v1.2 diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223data.bed new file mode 100644 index 00000000..8cac2e75 --- /dev/null +++ b/LiveBedfiles/Pan5223data.bed @@ -0,0 +1,1287 @@ +#2024-04-03 11:58:23.835019 +#Chr Start Stop EntrezID Gene_Accession +1 22404971 22405076 998 CDC42;NM_001791.4 +1 22408214 22408287 998 CDC42;NM_001791.4 +1 22412931 22413041 998 CDC42;NM_001791.4 +1 22413161 22413359 998 CDC42;NM_001791.4 +1 22417920 22418010 998 CDC42;NM_001791.4 +1 43803519 43803598 4352 MPL;NM_005373.3 +1 43803769 43803902 4352 MPL;NM_005373.3 +1 43804212 43804391 4352 MPL;NM_005373.3 +1 43804941 43805240 4352 MPL;NM_005373.3 +1 43805634 43805797 4352 MPL;NM_005373.3 +1 43806057 43806184 4352 MPL;NM_005373.3 +1 43812115 43812300 4352 MPL;NM_005373.3 +1 43812462 43812605 4352 MPL;NM_005373.3 +1 43814513 43814673 4352 MPL;NM_005373.3 +1 43814933 43815030 4352 MPL;NM_005373.3 +1 43817886 43817974 4352 MPL;NM_005373.3 +1 43818188 43818443 4352 MPL;NM_005373.3 +1 145507666 145507733 9939 RBM8A;NM_005105.5 +1 145508015 145508075 9939 RBM8A;NM_005105.5 +1 145508206 145508284 9939 RBM8A;NM_005105.5 +1 145508474 145508611 9939 RBM8A;NM_005105.5 +1 145508915 145509052 9939 RBM8A;NM_005105.5 +1 145509165 145509211 9939 RBM8A;NM_005105.5 +1 155204785 155204891 2629 GBA;NM_000157.4 +1 155204985 155205102 2629 GBA;NM_000157.4 +1 155205471 155205635 2629 GBA;NM_000157.4 +1 155206035 155206260 2629 GBA;NM_000157.4 +1 155207131 155207369 2629 GBA;NM_000157.4 +1 155207924 155208097 2629 GBA;NM_000157.4 +1 155208307 155208441 2629 GBA;NM_000157.4 +1 155209406 155209553 2629 GBA;NM_000157.4 +1 155209676 155209868 2629 GBA;NM_000157.4 +1 155210420 155210508 2629 GBA;NM_000157.4 +1 155210876 155210903 2629 GBA;NM_000157.4 +1 169483550 169483697 2153 F5;NM_000130.5 +1 169484681 169484864 2153 F5;NM_000130.5 +1 169487649 169487801 2153 F5;NM_000130.5 +1 169489757 169489902 2153 F5;NM_000130.5 +1 169492434 169492590 2153 F5;NM_000130.5 +1 169493038 169493142 2153 F5;NM_000130.5 +1 169494074 169494146 2153 F5;NM_000130.5 +1 169495138 169495255 2153 F5;NM_000130.5 +1 169497152 169497332 2153 F5;NM_000130.5 +1 169498845 169499056 2153 F5;NM_000130.5 +1 169500023 169500260 2153 F5;NM_000130.5 +1 169505743 169505918 2153 F5;NM_000130.5 +1 169509531 169512352 2153 F5;NM_000130.5 +1 169513533 169513746 2153 F5;NM_000130.5 +1 169515679 169515830 2153 F5;NM_000130.5 +1 169519038 169519253 2153 F5;NM_000130.5 +1 169519877 169519977 2153 F5;NM_000130.5 +1 169521794 169521972 2153 F5;NM_000130.5 +1 169524419 169524585 2153 F5;NM_000130.5 +1 169525883 169526105 2153 F5;NM_000130.5 +1 169528390 169528534 2153 F5;NM_000130.5 +1 169529791 169530004 2153 F5;NM_000130.5 +1 169541458 169541581 2153 F5;NM_000130.5 +1 169551668 169551760 2153 F5;NM_000130.5 +1 169555466 169555624 2153 F5;NM_000130.5 +1 186823486 186823519 5321 PLA2G4A;NM_024420.3 +1 186839566 186839648 5321 PLA2G4A;NM_024420.3 +1 186862142 186862291 5321 PLA2G4A;NM_024420.3 +1 186863229 186863343 5321 PLA2G4A;NM_024420.3 +1 186876096 186876134 5321 PLA2G4A;NM_024420.3 +1 186880379 186880521 5321 PLA2G4A;NM_024420.3 +1 186901894 186902031 5321 PLA2G4A;NM_024420.3 +1 186908139 186908362 5321 PLA2G4A;NM_024420.3 +1 186909111 186909226 5321 PLA2G4A;NM_024420.3 +1 186915768 186915906 5321 PLA2G4A;NM_024420.3 +1 186916000 186916093 5321 PLA2G4A;NM_024420.3 +1 186919788 186919860 5321 PLA2G4A;NM_024420.3 +1 186925233 186925476 5321 PLA2G4A;NM_024420.3 +1 186934540 186934725 5321 PLA2G4A;NM_024420.3 +1 186946724 186946920 5321 PLA2G4A;NM_024420.3 +1 186948446 186948604 5321 PLA2G4A;NM_024420.3 +1 186957508 186957640 5321 PLA2G4A;NM_024420.3 +1 197008507 197008541 2165 F13B;NM_001994.3 +1 197009651 197009865 2165 F13B;NM_001994.3 +1 197019826 197020009 2165 F13B;NM_001994.3 +1 197021763 197021964 2165 F13B;NM_001994.3 +1 197024844 197025027 2165 F13B;NM_001994.3 +1 197026142 197026328 2165 F13B;NM_001994.3 +1 197026415 197026595 2165 F13B;NM_001994.3 +1 197029495 197029672 2165 F13B;NM_001994.3 +1 197030028 197030205 2165 F13B;NM_001994.3 +1 197030913 197031099 2165 F13B;NM_001994.3 +1 197031986 197032187 2165 F13B;NM_001994.3 +1 197036289 197036353 2165 F13B;NM_001994.3 +1 235826239 235826378 1130 LYST;NM_000081.4 +1 235827283 235827355 1130 LYST;NM_000081.4 +1 235827764 235827921 1130 LYST;NM_000081.4 +1 235840390 235840488 1130 LYST;NM_000081.4 +1 235840779 235840919 1130 LYST;NM_000081.4 +1 235850248 235850347 1130 LYST;NM_000081.4 +1 235856649 235856786 1130 LYST;NM_000081.4 +1 235860382 235860572 1130 LYST;NM_000081.4 +1 235866046 235866277 1130 LYST;NM_000081.4 +1 235872390 235872608 1130 LYST;NM_000081.4 +1 235875356 235875497 1130 LYST;NM_000081.4 +1 235878500 235878657 1130 LYST;NM_000081.4 +1 235880011 235880078 1130 LYST;NM_000081.4 +1 235883960 235884205 1130 LYST;NM_000081.4 +1 235887327 235887480 1130 LYST;NM_000081.4 +1 235891375 235891431 1130 LYST;NM_000081.4 +1 235892895 235892957 1130 LYST;NM_000081.4 +1 235894146 235894243 1130 LYST;NM_000081.4 +1 235894331 235894477 1130 LYST;NM_000081.4 +1 235896802 235896991 1130 LYST;NM_000081.4 +1 235897129 235897206 1130 LYST;NM_000081.4 +1 235897782 235897959 1130 LYST;NM_000081.4 +1 235904721 235904928 1130 LYST;NM_000081.4 +1 235907278 235907457 1130 LYST;NM_000081.4 +1 235909635 235909827 1130 LYST;NM_000081.4 +1 235914509 235914662 1130 LYST;NM_000081.4 +1 235915304 235915471 1130 LYST;NM_000081.4 +1 235916343 235916574 1130 LYST;NM_000081.4 +1 235918777 235918947 1130 LYST;NM_000081.4 +1 235920580 235920758 1130 LYST;NM_000081.4 +1 235922271 235922899 1130 LYST;NM_000081.4 +1 235926019 235926151 1130 LYST;NM_000081.4 +1 235929378 235929577 1130 LYST;NM_000081.4 +1 235933459 235933597 1130 LYST;NM_000081.4 +1 235937141 235937291 1130 LYST;NM_000081.4 +1 235938212 235938386 1130 LYST;NM_000081.4 +1 235940362 235940608 1130 LYST;NM_000081.4 +1 235944164 235944355 1130 LYST;NM_000081.4 +1 235945226 235945387 1130 LYST;NM_000081.4 +1 235950499 235950673 1130 LYST;NM_000081.4 +1 235952000 235952145 1130 LYST;NM_000081.4 +1 235954998 235955425 1130 LYST;NM_000081.4 +1 235956802 235956912 1130 LYST;NM_000081.4 +1 235963619 235963686 1130 LYST;NM_000081.4 +1 235964170 235964397 1130 LYST;NM_000081.4 +1 235966207 235966364 1130 LYST;NM_000081.4 +1 235967803 235967965 1130 LYST;NM_000081.4 +1 235969042 235970072 1130 LYST;NM_000081.4 +1 235971754 235973834 1130 LYST;NM_000081.4 +1 235976270 235976361 1130 LYST;NM_000081.4 +1 235993525 235993717 1130 LYST;NM_000081.4 +2 44040254 44040448 64240 ABCG5;NM_022436.3 +2 44041615 44041728 64240 ABCG5;NM_022436.3 +2 44047053 44047239 64240 ABCG5;NM_022436.3 +2 44049935 44050074 64240 ABCG5;NM_022436.3 +2 44051051 44051257 64240 ABCG5;NM_022436.3 +2 44051357 44051571 64240 ABCG5;NM_022436.3 +2 44052027 44052157 64240 ABCG5;NM_022436.3 +2 44053520 44053660 64240 ABCG5;NM_022436.3 +2 44055121 44055254 64240 ABCG5;NM_022436.3 +2 44058907 44059006 64240 ABCG5;NM_022436.3 +2 44059085 44059222 64240 ABCG5;NM_022436.3 +2 44064972 44065094 64240 ABCG5;NM_022436.3 +2 44065675 44065818 64240 ABCG5;NM_022436.3 +2 44066192 44066255 64241 ABCG8;NM_022437.3 +2 44071645 44071747 64241 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MYH9;NM_002473.6 +X 48542242 48542374 7454 WAS;NM_000377.3 +X 48542671 48542812 7454 WAS;NM_000377.3 +X 48543935 48544022 7454 WAS;NM_000377.3 +X 48544122 48544225 7454 WAS;NM_000377.3 +X 48544334 48544376 7454 WAS;NM_000377.3 +X 48544469 48544523 7454 WAS;NM_000377.3 +X 48545169 48545344 7454 WAS;NM_000377.3 +X 48546442 48546485 7454 WAS;NM_000377.3 +X 48546688 48546842 7454 WAS;NM_000377.3 +X 48547048 48547455 7454 WAS;NM_000377.3 +X 48547708 48547823 7454 WAS;NM_000377.3 +X 48549497 48549553 7454 WAS;NM_000377.3 +X 48649516 48649736 2623 GATA1;NM_002049.4 +X 48650250 48650628 2623 GATA1;NM_002049.4 +X 48650729 48650875 2623 GATA1;NM_002049.4 +X 48651578 48651704 2623 GATA1;NM_002049.4 +X 48652199 48652571 2623 GATA1;NM_002049.4 +X 138612923 138613011 2158 F9;NM_000133.4 +X 138619168 138619332 2158 F9;NM_000133.4 +X 138619520 138619545 2158 F9;NM_000133.4 +X 138623234 138623348 2158 F9;NM_000133.4 +X 138630521 138630650 2158 F9;NM_000133.4 +X 138633220 138633423 2158 F9;NM_000133.4 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153586936 2316 FLNA;NM_001456.3 +X 153587351 153587522 2316 FLNA;NM_001456.3 +X 153587613 153587774 2316 FLNA;NM_001456.3 +X 153587851 153588014 2316 FLNA;NM_001456.3 +X 153588099 153588273 2316 FLNA;NM_001456.3 +X 153588357 153588955 2316 FLNA;NM_001456.3 +X 153589675 153589938 2316 FLNA;NM_001456.3 +X 153590037 153590155 2316 FLNA;NM_001456.3 +X 153590346 153590516 2316 FLNA;NM_001456.3 +X 153590609 153590700 2316 FLNA;NM_001456.3 +X 153590785 153590946 2316 FLNA;NM_001456.3 +X 153591028 153591152 2316 FLNA;NM_001456.3 +X 153592389 153592533 2316 FLNA;NM_001456.3 +X 153592626 153592740 2316 FLNA;NM_001456.3 +X 153592893 153593087 2316 FLNA;NM_001456.3 +X 153593188 153593325 2316 FLNA;NM_001456.3 +X 153593503 153593627 2316 FLNA;NM_001456.3 +X 153593716 153593854 2316 FLNA;NM_001456.3 +X 153594391 153594592 2316 FLNA;NM_001456.3 +X 153594675 153594838 2316 FLNA;NM_001456.3 +X 153594929 153595007 2316 FLNA;NM_001456.3 +X 153595099 153595218 2316 FLNA;NM_001456.3 +X 153595764 153595912 2316 FLNA;NM_001456.3 +X 153596008 153596106 2316 FLNA;NM_001456.3 +X 153596209 153596458 2316 FLNA;NM_001456.3 +X 153599240 153599613 2316 FLNA;NM_001456.3 +X 154065871 154066027 2157 F8;NM_000132.4 +X 154088706 154088883 2157 F8;NM_000132.4 +X 154089992 154090141 2157 F8;NM_000132.4 +X 154091357 154091502 2157 F8;NM_000132.4 +X 154124351 154124507 2157 F8;NM_000132.4 +X 154128140 154128226 2157 F8;NM_000132.4 +X 154129645 154129717 2157 F8;NM_000132.4 +X 154130325 154130442 2157 F8;NM_000132.4 +X 154132180 154132363 2157 F8;NM_000132.4 +X 154132570 154132799 2157 F8;NM_000132.4 +X 154133085 154133298 2157 F8;NM_000132.4 +X 154134694 154134848 2157 F8;NM_000132.4 +X 154156845 154159951 2157 F8;NM_000132.4 +X 154175972 154176182 2157 F8;NM_000132.4 +X 154182166 154182317 2157 F8;NM_000132.4 +X 154185231 154185446 2157 F8;NM_000132.4 +X 154189349 154189443 2157 F8;NM_000132.4 +X 154194244 154194416 2157 F8;NM_000132.4 +X 154194700 154194962 2157 F8;NM_000132.4 +X 154197605 154197827 2157 F8;NM_000132.4 +X 154212961 154213078 2157 F8;NM_000132.4 +X 154215511 154215580 2157 F8;NM_000132.4 +X 154221210 154221423 2157 F8;NM_000132.4 +X 154225247 154225370 2157 F8;NM_000132.4 +X 154227753 154227875 2157 F8;NM_000132.4 +X 154250684 154250827 2157 F8;NM_000132.4 diff --git a/LiveBedfiles/Pan5223dataRefSeqFormat.txt b/LiveBedfiles/Pan5223dataRefSeqFormat.txt new file mode 100644 index 00000000..67bbe1bd --- /dev/null +++ b/LiveBedfiles/Pan5223dataRefSeqFormat.txt @@ -0,0 +1,91 @@ +#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonSEnds score name2 cdsStartStat cdsEndStat exonFrames +998 CDC42;NM_001791.4 1 + 22404971 22418010 22404971 22418010 5 22404971,22408214,22412931,22413161,22417920 22405076,22408287,22413041,22413359,22418010 nan CDC42 nan nan 0,0,0,0,0 +4352 MPL;NM_005373.3 1 + 43803519 43818443 43803519 43818443 12 43803519,43803769,43804212,43804941,43805634,43806057,43812115,43812462,43814513,43814933,43817886,43818188 43803598,43803902,43804391,43805240,43805797,43806184,43812300,43812605,43814673,43815030,43817974,43818443 nan MPL nan nan 0,0,0,0,0,0,0,0,0,0,0,0 +9939 RBM8A;NM_005105.5 1 + 145507666 145509211 145507666 145509211 6 145507666,145508015,145508206,145508474,145508915,145509165 145507733,145508075,145508284,145508611,145509052,145509211 nan RBM8A nan nan 0,0,0,0,0,0 +2629 GBA;NM_000157.4 1 - 155204785 155210903 155204785 155210903 11 155204785,155204985,155205471,155206035,155207131,155207924,155208307,155209406,155209676,155210420,155210876 155204891,155205102,155205635,155206260,155207369,155208097,155208441,155209553,155209868,155210508,155210903 nan GBA nan nan 0,0,0,0,0,0,0,0,0,0,0 +2153 F5;NM_000130.5 1 - 169483550 169555624 169483550 169555624 25 169483550,169484681,169487649,169489757,169492434,169493038,169494074,169495138,169497152,169498845,169500023,169505743,169509531,169513533,169515679,169519038,169519877,169521794,169524419,169525883,169528390,169529791,169541458,169551668,169555466 169483697,169484864,169487801,169489902,169492590,169493142,169494146,169495255,169497332,169499056,169500260,169505918,169512352,169513746,169515830,169519253,169519977,169521972,169524585,169526105,169528534,169530004,169541581,169551760,169555624 nan F5 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +5321 PLA2G4A;NM_024420.3 1 + 186823486 186957640 186823486 186957640 17 186823486,186839566,186862142,186863229,186876096,186880379,186901894,186908139,186909111,186915768,186916000,186919788,186925233,186934540,186946724,186948446,186957508 186823519,186839648,186862291,186863343,186876134,186880521,186902031,186908362,186909226,186915906,186916093,186919860,186925476,186934725,186946920,186948604,186957640 nan PLA2G4A nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2165 F13B;NM_001994.3 1 - 197008507 197036353 197008507 197036353 12 197008507,197009651,197019826,197021763,197024844,197026142,197026415,197029495,197030028,197030913,197031986,197036289 197008541,197009865,197020009,197021964,197025027,197026328,197026595,197029672,197030205,197031099,197032187,197036353 nan F13B nan nan 0,0,0,0,0,0,0,0,0,0,0,0 +1130 LYST;NM_000081.4 1 - 235826239 235993717 235826239 235993717 51 235826239,235827283,235827764,235840390,235840779,235850248,235856649,235860382,235866046,235872390,235875356,235878500,235880011,235883960,235887327,235891375,235892895,235894146,235894331,235896802,235897129,235897782,235904721,235907278,235909635,235914509,235915304,235916343,235918777,235920580,235922271,235926019,235929378,235933459,235937141,235938212,235940362,235944164,235945226,235950499,235952000,235954998,235956802,235963619,235964170,235966207,235967803,235969042,235971754,235976270,235993525 235826378,235827355,235827921,235840488,235840919,235850347,235856786,235860572,235866277,235872608,235875497,235878657,235880078,235884205,235887480,235891431,235892957,235894243,235894477,235896991,235897206,235897959,235904928,235907457,235909827,235914662,235915471,235916574,235918947,235920758,235922899,235926151,235929577,235933597,235937291,235938386,235940608,235944355,235945387,235950673,235952145,235955425,235956912,235963686,235964397,235966364,235967965,235970072,235973834,235976361,235993717 nan LYST nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +64240 ABCG5;NM_022436.3 2 - 44040254 44065818 44040254 44065818 13 44040254,44041615,44047053,44049935,44051051,44051357,44052027,44053520,44055121,44058907,44059085,44064972,44065675 44040448,44041728,44047239,44050074,44051257,44051571,44052157,44053660,44055254,44059006,44059222,44065094,44065818 nan ABCG5 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 +64241 ABCG8;NM_022437.3 2 + 44066192 44105052 44066192 44105052 13 44066192,44071645,44073293,44078722,44079492,44079737,44099114,44099361,44100925,44101545,44102284,44104699,44104914 44066255,44071747,44073450,44078961,44079625,44080007,44099277,44099445,44101125,44101622,44102552,44104827,44105052 nan ABCG8 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 +90411 MCFD2;NM_139279.6 2 - 47132601 47136310 47132601 47136310 3 47132601,47134948,47136161 47132733,47135108,47136310 nan MCFD2 nan nan 0,0,0 +2677 GGCX;NM_000821.7 2 - 85777056 85788551 85777056 85788551 15 85777056,85777677,85778047,85778602,85778934,85779538,85780061,85780354,85781265,85782606,85783304,85785562,85786039,85787937,85788508 85777249,85777873,85778195,85778733,85779104,85779690,85780193,85780620,85781429,85782713,85783383,85785728,85786198,85788108,85788551 nan GGCX nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +1281 COL3A1;NM_000090.4 2 + 189839215 189876500 189839215 189876500 51 189839215,189849485,189849922,189850390,189851784,189852806,189853315,189854121,189854821,189855032,189855729,189856212,189856394,189856909,189857612,189858086,189858763,189858959,189859266,189859449,189859771,189860417,189860850,189861123,189861890,189862061,189862425,189862991,189863399,189864010,189864195,189864567,189866122,189866261,189867023,189867680,189868136,189868459,189868707,189868982,189870075,189870931,189871070,189871662,189872225,189872610,189872760,189873649,189874903,189875373,189876353 189839294,189849688,189849973,189850504,189851865,189852860,189853369,189854175,189854875,189855086,189855783,189856257,189856448,189856954,189857666,189858185,189858808,189859058,189859320,189859557,189859825,189860516,189860904,189861222,189861944,189862115,189862479,189863045,189863444,189864109,189864303,189864621,189866176,189866315,189867077,189867788,189868190,189868513,189868869,189869090,189870183,189870985,189871178,189871716,189872333,189872664,189872868,189873947,189875091,189875616,189876500 nan COL3A1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +23218 NBEAL2;NM_015175.3 3 + 47021351 47050810 47021351 47050810 54 47021351,47030158,47030331,47030574,47030749,47031000,47032708,47032895,47033329,47033964,47035426,47035944,47036521,47037203,47037421,47037760,47038240,47038443,47038748,47039050,47039556,47039952,47040206,47040448,47040804,47041119,47041378,47042490,47042768,47043178,47043409,47043860,47044134,47044446,47044663,47045305,47045566,47045984,47046461,47046670,47046978,47047227,47047435,47047654,47047822,47048555,47048730,47049014,47049305,47049559,47049772,47050009,47050478,47050708 47021402,47030247,47030460,47030656,47030871,47031083,47032794,47033178,47033436,47034045,47035510,47036043,47037123,47037336,47037541,47038082,47038323,47038536,47038923,47039184,47039716,47040055,47040369,47040607,47040964,47041205,47041894,47042669,47042928,47043316,47043778,47044010,47044292,47044571,47044799,47045466,47045883,47046080,47046586,47046811,47047109,47047337,47047553,47047752,47047939,47048645,47048840,47049187,47049400,47049676,47049931,47050158,47050614,47050810 nan NBEAL2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2815 GP9;NM_000174.5 3 + 128780582 128781116 128780582 128781116 1 128780582 128781116 nan GP9 nan nan 0 +84343 HPS3;NM_032383.5 3 + 148847510 148890009 148847510 148890009 17 148847510,148857790,148858803,148859081,148863140,148868385,148871280,148872893,148875136,148876452,148877832,148879934,148880476,148881628,148884820,148885679,148889881 148847727,148858285,148858975,148859167,148863333,148868467,148871435,148873002,148875318,148876633,148878066,148880120,148880665,148881736,148885027,148885770,148890009 nan HPS3 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +64805 P2RY12;NM_022788.5 3 - 151055604 151056633 151055604 151056633 1 151055604 151056633 nan P2RY12 nan nan 0 +2122 MECOM;NM_004991.4 3 - 168802696 169381160 168802696 169381160 17 168802696,168806787,168807787,168810745,168812863,168818672,168819847,168825713,168830574,168833170,168838843,168840367,168845631,168849216,168861485,169098974,169381123 168802831,168806971,168808024,168810890,168813033,168818750,168820014,168825740,168830662,168834527,168838997,168840515,168845848,168849319,168861620,169099312,169381160 nan MECOM nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +7066 THPO;NM_000460.4 3 - 184090300 184094047 184090300 184094047 5 184090300,184091202,184093302,184093675,184094034 184090966,184091370,184093389,184093803,184094047 nan THPO nan nan 0,0,0,0,0 +3827 KNG1;NM_001102416.3 3 + 186435331 186460120 186435331 186460120 10 186435331,186437893,186440225,186442876,186445025,186449333,186450290,186456887,186457116,186459310 186435526,186438004,186440310,186443049,186445133,186449418,186450463,186456995,186457203,186460120 nan KNG1 nan nan 0,0,0,0,0,0,0,0,0,0 +2244 FGB;NM_005141.5 4 + 155484170 155491802 155484170 155491802 8 155484170,155486959,155487640,155488744,155489532,155490333,155490665,155491570 155484284,155487151,155487824,155488972,155489646,155490459,155490951,155491802 nan FGB nan nan 0,0,0,0,0,0,0,0 +2243 FGA;NM_000508.5 4 - 155505275 155511839 155505275 155511839 6 155505275,155506689,155508663,155509944,155510588,155511785 155505985,155508070,155508809,155510128,155510714,155511839 nan FGA nan nan 0,0,0,0,0,0 +2266 FGG;NM_021870.3 4 - 155525985 155533761 155525985 155533761 9 155525985,155527856,155529617,155530781,155531218,155532956,155533169,155533542,155533683 155526218,155528134,155529802,155530915,155531349,155533050,155533353,155533587,155533761 nan FGG nan nan 0,0,0,0,0,0,0,0,0 +3818 KLKB1;NM_000892.5 4 + 187149349 187179366 187149349 187179366 14 187149349,187153280,187155105,187157934,187159409,187171396,187172372,187172640,187172902,187173170,187175741,187177145,187178379,187179174 187149407,187153443,187155212,187158094,187159519,187171556,187172482,187172803,187173015,187173339,187175917,187177241,187178519,187179366 nan KLKB1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2160 F11;NM_000128.4 4 + 187188290 187209768 187188290 187209768 14 187188290,187192762,187194224,187195269,187196940,187197384,187201165,187201376,187201627,187205245,187206791,187207568,187208837,187209606 187188345,187192925,187194331,187195429,187197050,187197544,187201275,187201539,187201734,187205414,187206967,187207664,187208977,187209768 nan F11 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2533 FYB1;NM_001465.6 5 - 39107544 39203062 39107544 39203062 18 39107544,39108332,39110457,39118975,39119636,39122437,39124354,39126099,39127842,39130691,39134309,39134956,39137701,39138758,39139334,39141196,39153549,39201927 39107567,39108364,39110491,39119138,39119736,39122504,39124380,39126237,39127909,39130714,39134451,39135116,39137822,39138793,39139354,39141243,39153706,39203062 nan FYB1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +8546 AP3B1;NM_003664.5 5 - 77298725 77590403 77298725 77590403 27 77298725,77311233,77316515,77330184,77334866,77385216,77396776,77406030,77409575,77411949,77423853,77424944,77436966,77452081,77458642,77461433,77471449,77471607,77473162,77477330,77511878,77521365,77523195,77523967,77536685,77563343,77590275 77298879,77311372,77316613,77330269,77335098,77385323,77396849,77406178,77409747,77412058,77423984,77425131,77437143,77452191,77458775,77461496,77471521,77471662,77473260,77477486,77512061,77521432,77523356,77524063,77536760,77563419,77590403 nan AP3B1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +1729 DIAPH1;NM_005219.5 5 - 140896417 140998481 140896417 140998481 28 140896417,140903709,140905604,140905863,140907139,140908019,140908268,140908738,140909169,140913901,140915620,140951492,140953058,140954533,140955796,140956322,140957041,140957791,140958081,140958654,140960310,140961878,140962772,140963051,140963690,140966608,140967790,140998364 140896575,140903796,140905740,140906028,140907264,140908149,140908508,140908840,140909264,140914000,140915629,140951607,140953775,140954713,140955861,140956438,140957158,140957910,140958192,140958763,140960450,140961942,140962859,140963182,140963792,140966764,140967817,140998481 nan DIAPH1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2161 F12;NM_000505.4 5 - 176829292 176836528 176829292 176836528 14 176829292,176829550,176830254,176830481,176830859,176831196,176831499,176831810,176832054,176832323,176832735,176832962,176836046,176836471 176829460,176829699,176830398,176830618,176831091,176831414,176831665,176831915,176832186,176832434,176832806,176833062,176836104,176836528 nan F12 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2162 F13A1;NM_000129.4 6 - 6145851 6318897 6145851 6318897 14 6145851,6152045,6167690,6174812,6182220,6196029,6197455,6222265,6224918,6248544,6251043,6266790,6305583,6318767 6146005,6152182,6167851,6175100,6182374,6196118,6197559,6222404,6225093,6248652,6251162,6267042,6305772,6318897 nan F13A1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 +84062 DTNBP1;NM_032122.5 6 - 15523205 15663100 15523205 15663100 10 15523205,15524756,15533470,15593289,15615497,15627573,15637974,15651543,15652317,15663044 15523450,15524900,15533626,15593312,15615630,15627706,15638035,15651594,15652371,15663100 nan DTNBP1 nan nan 0,0,0,0,0,0,0,0,0,0 +80739 MPIG6B;NM_138272.3 6 + 31691160 31692851 31691160 31692851 6 31691160,31691415,31691918,31692363,31692541,31692746 31691221,31691763,31692009,31692404,31692621,31692851 nan MPIG6B nan nan 0,0,0,0,0,0 +7148 TNXB;NM_019105.8 6 - 32009125 32065975 32009125 32065975 43 32009125,32009547,32009788,32010042,32010231,32010475,32010727,32010951,32011213,32011525,32011783,32012157,32012782,32013951,32015510,32016139,32017046,32017774,32020446,32021164,32023627,32024362,32025834,32029173,32029933,32032597,32035437,32036166,32036598,32037329,32037903,32039766,32041423,32046809,32049144,32049812,32052189,32053526,32056561,32056999,32062852,32063387,32065572 32009227,32009711,32009950,32010139,32010383,32010608,32010858,32011095,32011333,32011669,32011906,32012493,32013103,32014233,32015789,32016427,32017364,32018098,32020770,32021482,32023951,32024680,32026167,32029497,32030260,32032894,32035761,32036484,32036913,32037638,32038191,32040075,32041729,32047142,32049450,32050103,32052486,32053895,32056825,32057156,32062968,32065226,32065975 nan TNXB nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +60 ACTB;NM_001101.5 7 - 5567378 5569288 5567378 5569288 5 5567378,5567634,5567911,5568791,5569165 5567522,5567816,5568350,5569031,5569288 nan ACTB nan nan 0,0,0,0,0 +54205 CYCS;NM_018947.6 7 - 25163319 25163738 25163319 25163738 2 25163319,25163569 25163468,25163738 nan CYCS nan nan 0,0 +10095 ARPC1B;NM_005720.4 7 + 98983337 98992112 98983337 98992112 9 98983337,98984307,98985661,98987527,98988515,98988800,98990293,98991651,98992073 98983401,98984412,98985884,98987635,98988722,98988876,98990499,98991742,98992112 nan ARPC1B nan nan 0,0,0,0,0,0,0,0,0 +5054 SERPINE1;NM_000602.5 7 + 100771674 100780723 100771674 100780723 8 100771674,100773701,100775155,100776975,100778774,100778995,100780281,100780685 100771945,100773935,100775350,100777174,100778875,100779082,100780365,100780723 nan SERPINE1 nan nan 0,0,0,0,0,0,0,0 +6916 TBXAS1;NM_001061.7 7 + 139529189 139719899 139529189 139719899 13 139529189,139572033,139575383,139611023,139635989,139653166,139655257,139657432,139661717,139706890,139715522,139717470,139719824 139529278,139572127,139575436,139611120,139636106,139653255,139655406,139657563,139662032,139706982,139715660,139717633,139719899 nan TBXAS1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 +10020 GNE;NM_005476.7 9 - 36217361 36249352 36217361 36249352 11 36217361,36218179,36219834,36222773,36223369,36227244,36229017,36233916,36236828,36246027,36249188 36217597,36218296,36220017,36222995,36223499,36227455,36229105,36234129,36236981,36246479,36249352 nan GNE nan nan 0,0,0,0,0,0,0,0,0,0,0 +5742 PTGS1;NM_000962.4 9 + 125133363 125154823 125133363 125154823 11 125133363,125133464,125140177,125140711,125141053,125143649,125143942,125145787,125148724,125152476,125154467 125133370,125133551,125140294,125140852,125141197,125143831,125144026,125146034,125149011,125152624,125154823 nan PTGS1 nan nan 0,0,0,0,0,0,0,0,0,0,0 +2022 ENG;NM_001114753.3 9 - 130577960 130616634 130577960 130616634 15 130577960,130578221,130579427,130580398,130580994,130581900,130582178,130586582,130587078,130587509,130587973,130588788,130591965,130605372,130616567 130578085,130578332,130579482,130580656,130581111,130581939,130582316,130586725,130587253,130587636,130588139,130588951,130592106,130605524,130616634 nan ENG nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +8328 GFI1B;NM_004188.8 9 + 135862065 135866437 135862065 135866437 6 135862065,135862668,135863583,135864447,135865128,135866258 135862165,135862806,135863855,135864585,135865294,135866437 nan GFI1B nan nan 0,0,0,0,0,0 +22852 ANKRD26;NM_001256053.2 10 - 27294518 27389255 27294518 27389255 34 27294518,27295845,27301810,27303422,27306430,27311486,27313375,27317780,27318214,27322153,27323724,27326114,27326799,27328893,27332354,27333085,27335281,27337729,27342248,27349273,27349440,27350072,27352916,27355415,27356085,27366266,27366561,27368017,27371731,27375467,27381334,27382277,27382613,27389013 27294652,27295891,27302039,27303640,27306721,27311616,27313488,27317874,27318285,27322306,27324681,27326252,27326983,27329107,27332496,27333119,27335449,27337908,27342319,27349346,27349469,27350171,27353010,27355477,27356215,27366469,27366622,27368090,27371762,27375538,27381441,27382451,27382728,27389255 nan ANKRD26 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +5328 PLAU;NM_002658.6 10 + 75671313 75676323 75671313 75676323 10 75671313,75671798,75671972,75672681,75673047,75673296,75673737,75674533,75675008,75676146 75671370,75671826,75672080,75672856,75673139,75673516,75673886,75674674,75675157,75676323 nan PLAU nan nan 0,0,0,0,0,0,0,0,0,0 +3257 HPS1;NM_000195.5 10 - 100177320 100202997 100177320 100202997 18 100177320,100177931,100179801,100182125,100183359,100183509,100184069,100185297,100185574,100186971,100189329,100189547,100190327,100190887,100193739,100195028,100195391,100202880 100177483,100178014,100179915,100182270,100183425,100183644,100184131,100185477,100185742,100187021,100189399,100189646,100190427,100191048,100193848,100195171,100195529,100202997 nan HPS1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +79803 HPS6;NM_024747.6 10 + 103825231 103827559 103825231 103827559 1 103825231 103827559 nan HPS6 nan nan 0 +64376 IKZF5;NM_001271840.1 10 - 124753295 124758141 124753295 124758141 3 124753295,124755509,124758008 124754239,124755692,124758141 nan IKZF5 nan nan 0,0,0 +6786 STIM1;NM_003156.4 11 + 3877500 4113028 3877500 4113028 12 3877500,3988781,4045102,4076755,4080510,4091255,4095731,4103413,4104111,4104492,4107706,4112511 3877639,3988912,4045217,4076867,4080626,4091433,4095909,4103581,4104212,4104728,4107773,4113028 nan STIM1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0 +11234 HPS5;NM_181507.2 11 - 18301428 18339405 18301428 18339405 22 18301428,18303496,18305341,18306892,18308137,18309081,18309439,18312988,18314445,18316566,18317545,18318344,18319105,18320338,18322374,18326968,18327681,18330492,18332287,18332933,18333460,18339297 18301489,18303767,18305448,18307006,18308257,18309237,18309560,18313566,18314523,18316716,18317669,18318531,18319264,18320517,18322463,18327040,18327894,18330626,18332480,18332998,18333571,18339405 nan HPS5 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2147 F2;NM_000506.5 11 + 46740785 46760958 46740785 46760958 14 46740785,46741251,46742072,46742339,46744729,46744931,46747408,46748047,46748260,46749545,46750213,46750929,46760597,46760814 46740864,46741412,46742097,46742390,46744835,46745068,46747723,46748176,46748387,46749713,46750387,46751111,46760668,46760958 nan F2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 +83706 FERMT3;NM_031471.6 11 + 63974836 63990964 63974836 63990964 14 63974836,63978082,63978523,63978746,63979116,63986722,63986995,63987211,63987362,63987691,63987907,63988487,63990519,63990784 63974996,63978316,63978643,63978915,63979219,63986830,63987130,63987261,63987487,63987798,63988141,63988612,63990661,63990964 nan FERMT3 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 +10235 RASGRP2;NM_153819.1 11 - 64494773 64510338 64494773 64510338 15 64494773,64496334,64497233,64497524,64502583,64503013,64503374,64504224,64506831,64507107,64507484,64508419,64508910,64509481,64510265 64494832,64496514,64497270,64497666,64502699,64503136,64503452,64504506,64506948,64507281,64507635,64508551,64508973,64509584,64510338 nan RASGRP2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2313 FLI1;NM_002017.5 11 + 128564153 128680883 128564153 128680883 9 128564153,128628009,128638012,128642676,128651852,128675260,128677074,128679051,128680353 128564171,128628221,128638167,128642880,128651918,128675326,128677134,128679099,128680883 nan FLI1 nan nan 0,0,0,0,0,0,0,0,0 +7450 VWF;NM_000552.5 12 - 6058180 6232362 6058180 6232362 51 6058180,6058951,6061009,6061556,6062661,6076651,6077292,6078376,6080764,6085276,6090951,6092315,6094210,6094728,6100984,6103027,6103580,6105167,6120782,6121252,6122646,6125254,6125681,6125919,6127530,6131065,6131905,6132796,6134745,6135071,6138507,6140609,6143853,6145553,6153456,6155888,6161708,6166022,6167014,6172119,6173411,6174302,6180462,6181496,6182784,6184500,6204625,6219539,6220031,6230339,6232307 6058369,6059049,6061049,6061685,6062760,6076768,6077333,6078557,6080875,6085426,6091157,6092420,6094285,6094831,6101184,6103369,6103773,6105388,6120960,6121296,6122811,6125398,6125822,6126036,6128909,6131201,6132064,6132953,6134859,6135212,6138654,6140744,6143992,6145657,6153617,6155983,6161949,6166238,6167210,6172220,6173550,6174439,6180509,6181608,6182907,6184717,6204750,6219748,6220134,6230504,6232362 nan VWF nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +2120 ETV6;NM_001987.5 12 + 11803061 12043980 11803061 12043980 8 11803061,11905383,11992073,12006360,12022357,12037378,12038859,12043874 11803094,11905513,11992238,12006495,12022903,12037521,12038960,12043980 nan ETV6 nan nan 0,0,0,0,0,0,0,0 +196527 ANO6;NM_001025356.3 12 + 45610104 45823094 45610104 45823094 20 45610104,45695796,45725077,45740804,45741810,45742300,45744441,45751072,45761470,45771835,45781943,45784203,45795577,45796854,45797221,45803139,45810481,45814853,45816739,45822887 45610174,45695876,45725206,45740870,45742098,45742414,45744557,45751207,45761576,45771896,45782086,45784281,45795803,45797024,45797319,45803270,45810687,45815056,45816845,45823094 nan ANO6 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +94 ACVRL1;NM_001077401.2 12 + 52306258 52314677 52306258 52314677 9 52306258,52306882,52307342,52307757,52308222,52309008,52309819,52312768,52314542 52306319,52307134,52307554,52307857,52308369,52309284,52310017,52312899,52314677 nan ACVRL1 nan nan 0,0,0,0,0,0,0,0,0 +2155 F7;NM_000131.4 13 + 113760155 113773322 113760155 113773322 9 113760155,113761158,113765003,113768065,113768160,113769973,113771079,113771786,113772726 113760219,113761224,113765164,113768090,113768274,113770114,113771189,113771910,113773322 nan F7 nan nan 0,0,0,0,0,0,0,0,0 +2159 F10;NM_000504.4 13 + 113777169 113803831 113777169 113803831 8 113777169,113783765,113792770,113793670,113795232,113798164,113801692,113803229 113777239,113783926,113792795,113793784,113795364,113798409,113801810,113803831 nan F10 nan nan 0,0,0,0,0,0,0,0 +87 ACTN1;NM_001102.4 14 - 69341575 69445773 69341575 69445773 21 69341575,69343798,69345705,69346678,69347526,69349174,69349589,69350884,69351491,69352141,69356855,69358769,69360371,69369193,69371371,69376034,69376671,69378872,69387722,69392274,69445668 69341734,69343957,69345786,69346825,69347706,69349309,69349772,69351025,69351600,69352292,69357003,69359000,69360464,69369279,69371453,69376113,69376759,69378959,69387842,69392389,69445773 nan ACTN1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +63894 VIPAS39;NM_022067.4 14 - 77893958 77920445 77893958 77920445 19 77893958,77894712,77895348,77896023,77900184,77900604,77901601,77902186,77904150,77907408,77908902,77909461,77910591,77914836,77915635,77916056,77917529,77919641,77920352 77893979,77894817,77895438,77896110,77900274,77900646,77901736,77902262,77904224,77907436,77909005,77909495,77910684,77914893,77915700,77916095,77917676,77919744,77920445 nan VIPAS39 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +113189 CHST14;NM_130468.4 15 + 40763412 40764543 40763412 40764543 1 40763412 40764543 nan CHST14 nan nan 0 +26258 BLOC1S6;NM_012388.4 15 + 45879641 45898712 45879641 45898712 5 45879641,45884332,45895297,45897625,45898592 45879723,45884474,45895385,45897712,45898712 nan BLOC1S6 nan nan 0,0,0,0,0 +26276 VPS33B;NM_018668.5 15 - 91542204 91565479 91542204 91565479 23 91542204,91542906,91543129,91543719,91544618,91545279,91546314,91548106,91548284,91548609,91548923,91549202,91549601,91549881,91550179,91550698,91551099,91553030,91557033,91557613,91560192,91561034,91565383 91542284,91543023,91543205,91543821,91544692,91545412,91546361,91548161,91548349,91548684,91549014,91549289,91549675,91549959,91550276,91550803,91551194,91553076,91557101,91557663,91560254,91561115,91565479 nan VPS33B nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +79001 VKORC1;NM_024006.6 16 - 31102454 31106050 31102454 31106050 3 31102454,31104632,31105877 31102663,31104742,31106050 nan VKORC1 nan nan 0,0,0 +5345 SERPINF2;NM_000934.4 17 + 1648289 1657828 1648289 1657828 9 1648289,1648468,1648626,1649001,1650312,1650602,1651891,1655879,1657415 1648352,1648507,1648689,1649203,1650456,1650806,1652034,1656084,1657828 nan SERPINF2 nan nan 0,0,0,0,0,0,0,0,0 +2811 GP1BA;NM_000173.7 17 + 4835899 4837858 4835899 4837858 1 4835899 4837858 nan GP1BA nan nan 0 +342618 SLFN14;NM_001129820.2 17 - 33875257 33885081 33875257 33885081 4 33875257,33879748,33881594,33884021 33876092,33880463,33881723,33885081 nan SLFN14 nan nan 0,0,0,0 +3674 ITGA2B;NM_000419.5 17 - 42449731 42466841 42449731 42466841 30 42449731,42451721,42452026,42452365,42452958,42453200,42453452,42453675,42454376,42455065,42455729,42456010,42457056,42457369,42457613,42457753,42457967,42458246,42460860,42461261,42461452,42461678,42461905,42462315,42462531,42462653,42462918,42463191,42463377,42466653 42449791,42451838,42452128,42452479,42453084,42453353,42453552,42453756,42454456,42455158,42455877,42456078,42457182,42457521,42457669,42457858,42458013,42458429,42461072,42461314,42461506,42461722,42461953,42462444,42462577,42462703,42463084,42463289,42463499,42466841 nan ITGA2B nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +3690 ITGB3;NM_000212.3 17 + 45331227 45387570 45331227 45387570 15 45331227,45351784,45360719,45361808,45363625,45364435,45367046,45367550,45368319,45369504,45376673,45377843,45380086,45384836,45387504 45331306,45351870,45360915,45362061,45363788,45364597,45367142,45367640,45368454,45369934,45376896,45377944,45380206,45385003,45387570 nan ITGB3 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +3998 LMAN1;NM_005570.4 18 - 56998324 57026476 56998324 57026476 13 56998324,56998649,57000322,57005788,57005991,57013150,57014744,57016344,57020433,57021750,57022544,57022735,57026262 56998361,56998771,57000476,57005859,57006185,57013283,57014803,57016468,57020533,57021812,57022652,57022890,57026476 nan LMAN1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 +2531 KDSR;NM_002035.4 18 - 60999014 61034351 60999014 61034351 10 60999014,61002489,61006032,61011642,61018120,61022436,61022730,61026968,61030011,61034243 60999134,61002591,61006116,61011726,61018312,61022532,61022796,61027025,61030101,61034351 nan KDSR nan nan 0,0,0,0,0,0,0,0,0,0 +8943 AP3D1;NM_003938.8 19 - 2102171 2151333 2102171 2151333 30 2102171,2108685,2109084,2109871,2110134,2110705,2111283,2111677,2114123,2114746,2115217,2115536,2116205,2116603,2117220,2118599,2120860,2121161,2121732,2123356,2123828,2127150,2129088,2129316,2130406,2132469,2137009,2137725,2138617,2151237 2102267,2108765,2109206,2109957,2110223,2110895,2111331,2111827,2114301,2114820,2115417,2115612,2116277,2116745,2117366,2118831,2121091,2121310,2121878,2123405,2123878,2127200,2129162,2129456,2130536,2132577,2137090,2137806,2138713,2151333 nan AP3D1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +6915 TBXA2R;NM_001060.6 19 - 3595685 3600632 3595685 3600632 2 3595685,3599846 3595931,3600632 nan TBXA2R nan nan 0,0 +6813 STXBP2;NM_006949.4 19 + 7702035 7712696 7702035 7712696 19 7702035,7703611,7703904,7704616,7705616,7705785,7706590,7706919,7707088,7707314,7707651,7707868,7708050,7709499,7710082,7711134,7712047,7712239,7712610 7702072,7703661,7703986,7704693,7705695,7705889,7706739,7707004,7707219,7707422,7707709,7707934,7708131,7709638,7710192,7711230,7712133,7712397,7712696 nan STXBP2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 +7171 TPM4;NM_003290.3 19 + 16187375 16212156 16187375 16212156 8 16187375,16192722,16197232,16198836,16199854,16204345,16204493,16212073 16187507,16192856,16197350,16198907,16199930,16204408,16204563,16212156 nan TPM4 nan nan 0,0,0,0,0,0,0,0 +388552 BLOC1S3;NM_212550.5 19 + 45682554 45683163 45682554 45683163 1 45682554 45683163 nan BLOC1S3 nan nan 0 +51206 GP6;NM_001083899.2 19 - 55525449 55549604 55525449 55549604 8 55525449,55527046,55530019,55536585,55538945,55543506,55543873,55549570 55526533,55527101,55530079,55536639,55539230,55543764,55543906,55549604 nan GP6 nan nan 0,0,0,0,0,0,0,0 +7056 THBD;NM_000361.3 20 - 23028413 23030141 23028413 23030141 1 23028413 23030141 nan THBD nan nan 0 +6714 SRC;NM_005417.4 20 + 36012556 36031782 36012556 36031782 11 36012556,36014477,36022297,36022576,36024564,36026101,36028517,36030004,36030837,36031151,36031573 36012806,36014577,36022396,36022680,36024714,36026257,36028697,36030081,36030991,36031283,36031782 nan SRC nan nan 0,0,0,0,0,0,0,0,0,0,0 +81027 TUBB1;NM_030773.4 20 + 57594577 57599838 57594577 57599838 4 57594577,57597899,57598544,57598759 57594634,57598008,57598655,57599838 nan TUBB1 nan nan 0,0,0,0 +861 RUNX1;NM_001754.5 21 - 36164431 36421196 36164431 36421196 8 36164431,36171597,36206706,36231770,36252853,36259139,36265221,36421138 36164907,36171759,36206898,36231875,36253010,36259393,36265260,36421196 nan RUNX1 nan nan 0,0,0,0,0,0,0,0 +2812 GP1BB;NM_000407.5 22 + 19711092 19711987 19711092 19711987 2 19711092,19711376 19711102,19711987 nan GP1BB nan nan 0,0 +89781 HPS4;NM_022081.6 22 - 26849198 26877728 26849198 26877728 13 26849198,26853824,26854410,26859882,26861420,26862191,26864516,26866684,26868267,26868797,26872958,26875230,26877687 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F8;NM_000132.4 2157 +X 154197605 154197827 X-154197605-154197827 0 + F8;NM_000132.4 2157 +X 154212961 154213078 X-154212961-154213078 0 + F8;NM_000132.4 2157 +X 154215511 154215580 X-154215511-154215580 0 + F8;NM_000132.4 2157 +X 154221210 154221423 X-154221210-154221423 0 + F8;NM_000132.4 2157 +X 154225247 154225370 X-154225247-154225370 0 + F8;NM_000132.4 2157 +X 154227753 154227875 X-154227753-154227875 0 + F8;NM_000132.4 2157 +X 154250684 154250827 X-154250684-154250827 0 + F8;NM_000132.4 2157 From a3d1168091d2af40efe0968ac7f5c31efcec5308 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:46:09 +0100 Subject: [PATCH 04/11] add Pan3608 --- LiveBedfiles/Pan5223_LogFile.md | 3 +++ LiveBedfiles/Pan5223data.bed | 12 ++++++++++++ 2 files changed, 15 insertions(+) diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index 09a57682..b297f752 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -23,3 +23,6 @@ RefSeq table format version generated as /home/dnanexus/out/Output_files/Pan5223 cruzdb module file path: /home/dnanexus/anaconda2/lib/python2.7/site-packages/cruzdb/__init__.py version as defined by git tag = v1.2 + +# Add additional panels +cat Pan3608.bed >> Pan5223data.bed diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223data.bed index 8cac2e75..49a4a2ba 100644 --- a/LiveBedfiles/Pan5223data.bed +++ b/LiveBedfiles/Pan5223data.bed @@ -1285,3 +1285,15 @@ X 154221210 154221423 2157 F8;NM_000132.4 X 154225247 154225370 2157 F8;NM_000132.4 X 154227753 154227875 2157 F8;NM_000132.4 X 154250684 154250827 2157 F8;NM_000132.4 +1 55038099 55038299 CNV12_1 +2 112805963 112806163 CNV14_1 +5 13763956 13764156 CNV15 +6 160243267 160243467 CNV16_1 +10 90869951 90870151 CNV02_1 +10 90875132 90875332 CNV03 +10 90905302 90905502 CNV07 +11 126373957 126374157 CNV08 +14 103715862 103716062 CNV09_1 +17 28745696 28745896 CNV10_1 +19 10869817 10870017 CNV11 +20 10643041 10643241 CNV13 From 8d73c1bf18954ce3a4700f685bffe6ee3eb3c42a Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:47:27 +0100 Subject: [PATCH 05/11] sort and rename --- LiveBedfiles/Pan5223_LogFile.md | 5 ++++- LiveBedfiles/Pan5223data.bed | 28 ++++++++++++++-------------- 2 files changed, 18 insertions(+), 15 deletions(-) diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index b297f752..fada1914 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -1,5 +1,5 @@ # Pan5223 -This bedfile will be used to perform the variant filtering step of exome depth for R90. It is a remake of Pan5171; it is a known issue that mokabed mapps exon 18 of DIAPH1 incorrectly. While this issue was manually rectified in the VCP3 readcount bedfile (Pan5217), it was not corrected in Pan5171. +This bedfile will be used to perform the variant filtering step of exome depth for R90. It is a remake of Pan5223; it is a known issue that mokabed mapps exon 18 of DIAPH1 incorrectly. While this issue was manually rectified in the VCP3 readcount bedfile (Pan5217), it was not corrected in Pan5171. Additionally, TBXA2R will be updated to use the MANE transcript NM_001060. @@ -26,3 +26,6 @@ version as defined by git tag = v1.2 # Add additional panels cat Pan3608.bed >> Pan5223data.bed + +## Sort data.bed +sort Pan5223data.bed -k1,1V -k2,2n -k3,3n > Pan5223_sorted.bed;mv Pan5223data.bed Pan5223_unsorted.bed; mv Pan5223_sorted.bed Pan5223data.bed; rm Pan5223_unsorted.bed \ No newline at end of file diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223data.bed index 49a4a2ba..1d5b762c 100644 --- a/LiveBedfiles/Pan5223data.bed +++ b/LiveBedfiles/Pan5223data.bed @@ -1,5 +1,3 @@ -#2024-04-03 11:58:23.835019 -#Chr Start Stop EntrezID Gene_Accession 1 22404971 22405076 998 CDC42;NM_001791.4 1 22408214 22408287 998 CDC42;NM_001791.4 1 22412931 22413041 998 CDC42;NM_001791.4 @@ -17,6 +15,7 @@ 1 43814933 43815030 4352 MPL;NM_005373.3 1 43817886 43817974 4352 MPL;NM_005373.3 1 43818188 43818443 4352 MPL;NM_005373.3 +1 55038099 55038299 CNV12_1 1 145507666 145507733 9939 RBM8A;NM_005105.5 1 145508015 145508075 9939 RBM8A;NM_005105.5 1 145508206 145508284 9939 RBM8A;NM_005105.5 @@ -183,6 +182,7 @@ 2 85786039 85786198 2677 GGCX;NM_000821.7 2 85787937 85788108 2677 GGCX;NM_000821.7 2 85788508 85788551 2677 GGCX;NM_000821.7 +2 112805963 112806163 CNV14_1 2 189839215 189839294 1281 COL3A1;NM_000090.4 2 189849485 189849688 1281 COL3A1;NM_000090.4 2 189849922 189849973 1281 COL3A1;NM_000090.4 @@ -390,6 +390,7 @@ 4 187207568 187207664 2160 F11;NM_000128.4 4 187208837 187208977 2160 F11;NM_000128.4 4 187209606 187209768 2160 F11;NM_000128.4 +5 13763956 13764156 CNV15 5 39107544 39107567 2533 FYB1;NM_001465.6 5 39108332 39108364 2533 FYB1;NM_001465.6 5 39110457 39110491 2533 FYB1;NM_001465.6 @@ -550,6 +551,7 @@ 6 32062852 32062968 7148 TNXB;NM_019105.8 6 32063387 32065226 7148 TNXB;NM_019105.8 6 32065572 32065975 7148 TNXB;NM_019105.8 +6 160243267 160243467 CNV16_1 7 5567378 5567522 60 ACTB;NM_001101.5 7 5567634 5567816 60 ACTB;NM_001101.5 7 5567911 5568350 60 ACTB;NM_001101.5 @@ -674,6 +676,9 @@ 10 75674533 75674674 5328 PLAU;NM_002658.6 10 75675008 75675157 5328 PLAU;NM_002658.6 10 75676146 75676323 5328 PLAU;NM_002658.6 +10 90869951 90870151 CNV02_1 +10 90875132 90875332 CNV03 +10 90905302 90905502 CNV07 10 100177320 100177483 3257 HPS1;NM_000195.5 10 100177931 100178014 3257 HPS1;NM_000195.5 10 100179801 100179915 3257 HPS1;NM_000195.5 @@ -773,6 +778,7 @@ 11 64508910 64508973 10235 RASGRP2;NM_153819.1 11 64509481 64509584 10235 RASGRP2;NM_153819.1 11 64510265 64510338 10235 RASGRP2;NM_153819.1 +11 126373957 126374157 CNV08 11 128564153 128564171 2313 FLI1;NM_002017.5 11 128628009 128628221 2313 FLI1;NM_002017.5 11 128638012 128638167 2313 FLI1;NM_002017.5 @@ -927,6 +933,7 @@ 14 77917529 77917676 63894 VIPAS39;NM_022067.4 14 77919641 77919744 63894 VIPAS39;NM_022067.4 14 77920352 77920445 63894 VIPAS39;NM_022067.4 +14 103715862 103716062 CNV09_1 15 40763412 40764543 113189 CHST14;NM_130468.4 15 45879641 45879723 26258 BLOC1S6;NM_012388.4 15 45884332 45884474 26258 BLOC1S6;NM_012388.4 @@ -969,6 +976,7 @@ 17 1655879 1656084 5345 SERPINF2;NM_000934.4 17 1657415 1657828 5345 SERPINF2;NM_000934.4 17 4835899 4837858 2811 GP1BA;NM_000173.7 +17 28745696 28745896 CNV10_1 17 33875257 33876092 342618 SLFN14;NM_001129820.2 17 33879748 33880463 342618 SLFN14;NM_001129820.2 17 33881594 33881723 342618 SLFN14;NM_001129820.2 @@ -1092,6 +1100,7 @@ 19 7712047 7712133 6813 STXBP2;NM_006949.4 19 7712239 7712397 6813 STXBP2;NM_006949.4 19 7712610 7712696 6813 STXBP2;NM_006949.4 +19 10869817 10870017 CNV11 19 16187375 16187507 7171 TPM4;NM_003290.3 19 16192722 16192856 7171 TPM4;NM_003290.3 19 16197232 16197350 7171 TPM4;NM_003290.3 @@ -1109,6 +1118,7 @@ 19 55543506 55543764 51206 GP6;NM_001083899.2 19 55543873 55543906 51206 GP6;NM_001083899.2 19 55549570 55549604 51206 GP6;NM_001083899.2 +20 10643041 10643241 CNV13 20 23028413 23030141 7056 THBD;NM_000361.3 20 36012556 36012806 6714 SRC;NM_005417.4 20 36014477 36014577 6714 SRC;NM_005417.4 @@ -1285,15 +1295,5 @@ X 154221210 154221423 2157 F8;NM_000132.4 X 154225247 154225370 2157 F8;NM_000132.4 X 154227753 154227875 2157 F8;NM_000132.4 X 154250684 154250827 2157 F8;NM_000132.4 -1 55038099 55038299 CNV12_1 -2 112805963 112806163 CNV14_1 -5 13763956 13764156 CNV15 -6 160243267 160243467 CNV16_1 -10 90869951 90870151 CNV02_1 -10 90875132 90875332 CNV03 -10 90905302 90905502 CNV07 -11 126373957 126374157 CNV08 -14 103715862 103716062 CNV09_1 -17 28745696 28745896 CNV10_1 -19 10869817 10870017 CNV11 -20 10643041 10643241 CNV13 +#2024-04-03 11:58:23.835019 +#Chr Start Stop EntrezID Gene_Accession From d92fdccc91aebf00bf1129f9b4394cab6a18435c Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:48:23 +0100 Subject: [PATCH 06/11] remove header --- LiveBedfiles/Pan5223_LogFile.md | 4 +++- LiveBedfiles/Pan5223data.bed | 2 -- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index fada1914..749fc7cc 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -28,4 +28,6 @@ version as defined by git tag = v1.2 cat Pan3608.bed >> Pan5223data.bed ## Sort data.bed -sort Pan5223data.bed -k1,1V -k2,2n -k3,3n > Pan5223_sorted.bed;mv Pan5223data.bed Pan5223_unsorted.bed; mv Pan5223_sorted.bed Pan5223data.bed; rm Pan5223_unsorted.bed \ No newline at end of file +sort Pan5223data.bed -k1,1V -k2,2n -k3,3n > Pan5223_sorted.bed;mv Pan5223data.bed Pan5223_unsorted.bed; mv Pan5223_sorted.bed Pan5223data.bed; rm Pan5223_unsorted.bed + +remove header \ No newline at end of file diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223data.bed index 1d5b762c..5b4a367b 100644 --- a/LiveBedfiles/Pan5223data.bed +++ b/LiveBedfiles/Pan5223data.bed @@ -1295,5 +1295,3 @@ X 154221210 154221423 2157 F8;NM_000132.4 X 154225247 154225370 2157 F8;NM_000132.4 X 154227753 154227875 2157 F8;NM_000132.4 X 154250684 154250827 2157 F8;NM_000132.4 -#2024-04-03 11:58:23.835019 -#Chr Start Stop EntrezID Gene_Accession From 04886c82975c934585b212f5abaa020b59e9fb06 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:56:00 +0100 Subject: [PATCH 07/11] fix DIAPH1 --- LiveBedfiles/Pan5223_LogFile.md | 9 ++++++++- LiveBedfiles/Pan5223data.bed | 2 +- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index 749fc7cc..ce57a21b 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -30,4 +30,11 @@ cat Pan3608.bed >> Pan5223data.bed ## Sort data.bed sort Pan5223data.bed -k1,1V -k2,2n -k3,3n > Pan5223_sorted.bed;mv Pan5223data.bed Pan5223_unsorted.bed; mv Pan5223_sorted.bed Pan5223data.bed; rm Pan5223_unsorted.bed -remove header \ No newline at end of file +remove header + +## Fix DIAPH1 (no padding) +incorrect 5:140915620-140915629 + +corrected to 5:140950994-140951003 + + diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223data.bed index 5b4a367b..7ef5d1c4 100644 --- a/LiveBedfiles/Pan5223data.bed +++ b/LiveBedfiles/Pan5223data.bed @@ -446,7 +446,7 @@ 5 140908738 140908840 1729 DIAPH1;NM_005219.5 5 140909169 140909264 1729 DIAPH1;NM_005219.5 5 140913901 140914000 1729 DIAPH1;NM_005219.5 -5 140915620 140915629 1729 DIAPH1;NM_005219.5 +5 140950994 140951003 1729 DIAPH1;NM_005219.5 5 140951492 140951607 1729 DIAPH1;NM_005219.5 5 140953058 140953775 1729 DIAPH1;NM_005219.5 5 140954533 140954713 1729 DIAPH1;NM_005219.5 From f66fd0e3b6090f0db50fcd3595bd9cfd847e735f Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:57:44 +0100 Subject: [PATCH 08/11] convert to 4 col --- LiveBedfiles/Pan5223_LogFile.md | 2 + LiveBedfiles/Pan5223data.bed | 2570 +++++++++++++++---------------- 2 files changed, 1287 insertions(+), 1285 deletions(-) diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index ce57a21b..6cef187a 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -38,3 +38,5 @@ incorrect 5:140915620-140915629 corrected to 5:140950994-140951003 +## Convert to 4 column format +cut -f 1-4 Pan5223data.bed > Pan5223data_4col.bed; rm Pan5223data.bed; mv Pan5223data_4col.bed Pan5223data.bed \ No newline at end of file diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223data.bed index 7ef5d1c4..8ed43766 100644 --- a/LiveBedfiles/Pan5223data.bed +++ b/LiveBedfiles/Pan5223data.bed @@ -1,1297 +1,1297 @@ -1 22404971 22405076 998 CDC42;NM_001791.4 -1 22408214 22408287 998 CDC42;NM_001791.4 -1 22412931 22413041 998 CDC42;NM_001791.4 -1 22413161 22413359 998 CDC42;NM_001791.4 -1 22417920 22418010 998 CDC42;NM_001791.4 -1 43803519 43803598 4352 MPL;NM_005373.3 -1 43803769 43803902 4352 MPL;NM_005373.3 -1 43804212 43804391 4352 MPL;NM_005373.3 -1 43804941 43805240 4352 MPL;NM_005373.3 -1 43805634 43805797 4352 MPL;NM_005373.3 -1 43806057 43806184 4352 MPL;NM_005373.3 -1 43812115 43812300 4352 MPL;NM_005373.3 -1 43812462 43812605 4352 MPL;NM_005373.3 -1 43814513 43814673 4352 MPL;NM_005373.3 -1 43814933 43815030 4352 MPL;NM_005373.3 -1 43817886 43817974 4352 MPL;NM_005373.3 -1 43818188 43818443 4352 MPL;NM_005373.3 +1 22404971 22405076 998 +1 22408214 22408287 998 +1 22412931 22413041 998 +1 22413161 22413359 998 +1 22417920 22418010 998 +1 43803519 43803598 4352 +1 43803769 43803902 4352 +1 43804212 43804391 4352 +1 43804941 43805240 4352 +1 43805634 43805797 4352 +1 43806057 43806184 4352 +1 43812115 43812300 4352 +1 43812462 43812605 4352 +1 43814513 43814673 4352 +1 43814933 43815030 4352 +1 43817886 43817974 4352 +1 43818188 43818443 4352 1 55038099 55038299 CNV12_1 -1 145507666 145507733 9939 RBM8A;NM_005105.5 -1 145508015 145508075 9939 RBM8A;NM_005105.5 -1 145508206 145508284 9939 RBM8A;NM_005105.5 -1 145508474 145508611 9939 RBM8A;NM_005105.5 -1 145508915 145509052 9939 RBM8A;NM_005105.5 -1 145509165 145509211 9939 RBM8A;NM_005105.5 -1 155204785 155204891 2629 GBA;NM_000157.4 -1 155204985 155205102 2629 GBA;NM_000157.4 -1 155205471 155205635 2629 GBA;NM_000157.4 -1 155206035 155206260 2629 GBA;NM_000157.4 -1 155207131 155207369 2629 GBA;NM_000157.4 -1 155207924 155208097 2629 GBA;NM_000157.4 -1 155208307 155208441 2629 GBA;NM_000157.4 -1 155209406 155209553 2629 GBA;NM_000157.4 -1 155209676 155209868 2629 GBA;NM_000157.4 -1 155210420 155210508 2629 GBA;NM_000157.4 -1 155210876 155210903 2629 GBA;NM_000157.4 -1 169483550 169483697 2153 F5;NM_000130.5 -1 169484681 169484864 2153 F5;NM_000130.5 -1 169487649 169487801 2153 F5;NM_000130.5 -1 169489757 169489902 2153 F5;NM_000130.5 -1 169492434 169492590 2153 F5;NM_000130.5 -1 169493038 169493142 2153 F5;NM_000130.5 -1 169494074 169494146 2153 F5;NM_000130.5 -1 169495138 169495255 2153 F5;NM_000130.5 -1 169497152 169497332 2153 F5;NM_000130.5 -1 169498845 169499056 2153 F5;NM_000130.5 -1 169500023 169500260 2153 F5;NM_000130.5 -1 169505743 169505918 2153 F5;NM_000130.5 -1 169509531 169512352 2153 F5;NM_000130.5 -1 169513533 169513746 2153 F5;NM_000130.5 -1 169515679 169515830 2153 F5;NM_000130.5 -1 169519038 169519253 2153 F5;NM_000130.5 -1 169519877 169519977 2153 F5;NM_000130.5 -1 169521794 169521972 2153 F5;NM_000130.5 -1 169524419 169524585 2153 F5;NM_000130.5 -1 169525883 169526105 2153 F5;NM_000130.5 -1 169528390 169528534 2153 F5;NM_000130.5 -1 169529791 169530004 2153 F5;NM_000130.5 -1 169541458 169541581 2153 F5;NM_000130.5 -1 169551668 169551760 2153 F5;NM_000130.5 -1 169555466 169555624 2153 F5;NM_000130.5 -1 186823486 186823519 5321 PLA2G4A;NM_024420.3 -1 186839566 186839648 5321 PLA2G4A;NM_024420.3 -1 186862142 186862291 5321 PLA2G4A;NM_024420.3 -1 186863229 186863343 5321 PLA2G4A;NM_024420.3 -1 186876096 186876134 5321 PLA2G4A;NM_024420.3 -1 186880379 186880521 5321 PLA2G4A;NM_024420.3 -1 186901894 186902031 5321 PLA2G4A;NM_024420.3 -1 186908139 186908362 5321 PLA2G4A;NM_024420.3 -1 186909111 186909226 5321 PLA2G4A;NM_024420.3 -1 186915768 186915906 5321 PLA2G4A;NM_024420.3 -1 186916000 186916093 5321 PLA2G4A;NM_024420.3 -1 186919788 186919860 5321 PLA2G4A;NM_024420.3 -1 186925233 186925476 5321 PLA2G4A;NM_024420.3 -1 186934540 186934725 5321 PLA2G4A;NM_024420.3 -1 186946724 186946920 5321 PLA2G4A;NM_024420.3 -1 186948446 186948604 5321 PLA2G4A;NM_024420.3 -1 186957508 186957640 5321 PLA2G4A;NM_024420.3 -1 197008507 197008541 2165 F13B;NM_001994.3 -1 197009651 197009865 2165 F13B;NM_001994.3 -1 197019826 197020009 2165 F13B;NM_001994.3 -1 197021763 197021964 2165 F13B;NM_001994.3 -1 197024844 197025027 2165 F13B;NM_001994.3 -1 197026142 197026328 2165 F13B;NM_001994.3 -1 197026415 197026595 2165 F13B;NM_001994.3 -1 197029495 197029672 2165 F13B;NM_001994.3 -1 197030028 197030205 2165 F13B;NM_001994.3 -1 197030913 197031099 2165 F13B;NM_001994.3 -1 197031986 197032187 2165 F13B;NM_001994.3 -1 197036289 197036353 2165 F13B;NM_001994.3 -1 235826239 235826378 1130 LYST;NM_000081.4 -1 235827283 235827355 1130 LYST;NM_000081.4 -1 235827764 235827921 1130 LYST;NM_000081.4 -1 235840390 235840488 1130 LYST;NM_000081.4 -1 235840779 235840919 1130 LYST;NM_000081.4 -1 235850248 235850347 1130 LYST;NM_000081.4 -1 235856649 235856786 1130 LYST;NM_000081.4 -1 235860382 235860572 1130 LYST;NM_000081.4 -1 235866046 235866277 1130 LYST;NM_000081.4 -1 235872390 235872608 1130 LYST;NM_000081.4 -1 235875356 235875497 1130 LYST;NM_000081.4 -1 235878500 235878657 1130 LYST;NM_000081.4 -1 235880011 235880078 1130 LYST;NM_000081.4 -1 235883960 235884205 1130 LYST;NM_000081.4 -1 235887327 235887480 1130 LYST;NM_000081.4 -1 235891375 235891431 1130 LYST;NM_000081.4 -1 235892895 235892957 1130 LYST;NM_000081.4 -1 235894146 235894243 1130 LYST;NM_000081.4 -1 235894331 235894477 1130 LYST;NM_000081.4 -1 235896802 235896991 1130 LYST;NM_000081.4 -1 235897129 235897206 1130 LYST;NM_000081.4 -1 235897782 235897959 1130 LYST;NM_000081.4 -1 235904721 235904928 1130 LYST;NM_000081.4 -1 235907278 235907457 1130 LYST;NM_000081.4 -1 235909635 235909827 1130 LYST;NM_000081.4 -1 235914509 235914662 1130 LYST;NM_000081.4 -1 235915304 235915471 1130 LYST;NM_000081.4 -1 235916343 235916574 1130 LYST;NM_000081.4 -1 235918777 235918947 1130 LYST;NM_000081.4 -1 235920580 235920758 1130 LYST;NM_000081.4 -1 235922271 235922899 1130 LYST;NM_000081.4 -1 235926019 235926151 1130 LYST;NM_000081.4 -1 235929378 235929577 1130 LYST;NM_000081.4 -1 235933459 235933597 1130 LYST;NM_000081.4 -1 235937141 235937291 1130 LYST;NM_000081.4 -1 235938212 235938386 1130 LYST;NM_000081.4 -1 235940362 235940608 1130 LYST;NM_000081.4 -1 235944164 235944355 1130 LYST;NM_000081.4 -1 235945226 235945387 1130 LYST;NM_000081.4 -1 235950499 235950673 1130 LYST;NM_000081.4 -1 235952000 235952145 1130 LYST;NM_000081.4 -1 235954998 235955425 1130 LYST;NM_000081.4 -1 235956802 235956912 1130 LYST;NM_000081.4 -1 235963619 235963686 1130 LYST;NM_000081.4 -1 235964170 235964397 1130 LYST;NM_000081.4 -1 235966207 235966364 1130 LYST;NM_000081.4 -1 235967803 235967965 1130 LYST;NM_000081.4 -1 235969042 235970072 1130 LYST;NM_000081.4 -1 235971754 235973834 1130 LYST;NM_000081.4 -1 235976270 235976361 1130 LYST;NM_000081.4 -1 235993525 235993717 1130 LYST;NM_000081.4 -2 44040254 44040448 64240 ABCG5;NM_022436.3 -2 44041615 44041728 64240 ABCG5;NM_022436.3 -2 44047053 44047239 64240 ABCG5;NM_022436.3 -2 44049935 44050074 64240 ABCG5;NM_022436.3 -2 44051051 44051257 64240 ABCG5;NM_022436.3 -2 44051357 44051571 64240 ABCG5;NM_022436.3 -2 44052027 44052157 64240 ABCG5;NM_022436.3 -2 44053520 44053660 64240 ABCG5;NM_022436.3 -2 44055121 44055254 64240 ABCG5;NM_022436.3 -2 44058907 44059006 64240 ABCG5;NM_022436.3 -2 44059085 44059222 64240 ABCG5;NM_022436.3 -2 44064972 44065094 64240 ABCG5;NM_022436.3 -2 44065675 44065818 64240 ABCG5;NM_022436.3 -2 44066192 44066255 64241 ABCG8;NM_022437.3 -2 44071645 44071747 64241 ABCG8;NM_022437.3 -2 44073293 44073450 64241 ABCG8;NM_022437.3 -2 44078722 44078961 64241 ABCG8;NM_022437.3 -2 44079492 44079625 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d7f19cdf8344e9280164650c981a14f02e09b3ec Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 15:58:58 +0100 Subject: [PATCH 09/11] rename to cnv.bed --- LiveBedfiles/{Pan5223data.bed => Pan5223_CNV.bed} | 0 LiveBedfiles/Pan5223_LogFile.md | 6 ++++-- 2 files changed, 4 insertions(+), 2 deletions(-) rename LiveBedfiles/{Pan5223data.bed => Pan5223_CNV.bed} (100%) diff --git a/LiveBedfiles/Pan5223data.bed b/LiveBedfiles/Pan5223_CNV.bed similarity index 100% rename from LiveBedfiles/Pan5223data.bed rename to LiveBedfiles/Pan5223_CNV.bed diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index 6cef187a..1e65d2cf 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -37,6 +37,8 @@ incorrect 5:140915620-140915629 corrected to 5:140950994-140951003 - ## Convert to 4 column format -cut -f 1-4 Pan5223data.bed > Pan5223data_4col.bed; rm Pan5223data.bed; mv Pan5223data_4col.bed Pan5223data.bed \ No newline at end of file +cut -f 1-4 Pan5223data.bed > Pan5223data_4col.bed; rm Pan5223data.bed; mv Pan5223data_4col.bed Pan5223data.bed + +## Rename to _cnv.bed +git mv Pan5223data.bed Pan5223_CNV.bed \ No newline at end of file From 70873160d619fe9a769ac432788280e7b5977b31 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Wed, 3 Apr 2024 16:02:54 +0100 Subject: [PATCH 10/11] delete unrequired files --- LiveBedfiles/Pan5223_LogFile.md | 5 +- LiveBedfiles/Pan5223dataRefSeqFormat.txt | 91 -- LiveBedfiles/Pan5223dataSambamba.bed | 1285 ---------------------- 3 files changed, 4 insertions(+), 1377 deletions(-) delete mode 100644 LiveBedfiles/Pan5223dataRefSeqFormat.txt delete mode 100644 LiveBedfiles/Pan5223dataSambamba.bed diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index 1e65d2cf..a1f180e0 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -41,4 +41,7 @@ corrected to 5:140950994-140951003 cut -f 1-4 Pan5223data.bed > Pan5223data_4col.bed; rm Pan5223data.bed; mv Pan5223data_4col.bed Pan5223data.bed ## Rename to _cnv.bed -git mv Pan5223data.bed Pan5223_CNV.bed \ No newline at end of file +git mv Pan5223data.bed Pan5223_CNV.bed + +## Delete unrequired files +git rm Pan5223dataSambamba.bed Pan5223dataRefSeqFormat.txt \ No newline at end of file diff --git a/LiveBedfiles/Pan5223dataRefSeqFormat.txt b/LiveBedfiles/Pan5223dataRefSeqFormat.txt deleted file mode 100644 index 67bbe1bd..00000000 --- a/LiveBedfiles/Pan5223dataRefSeqFormat.txt +++ /dev/null @@ -1,91 +0,0 @@ -#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonSEnds score name2 cdsStartStat cdsEndStat exonFrames -998 CDC42;NM_001791.4 1 + 22404971 22418010 22404971 22418010 5 22404971,22408214,22412931,22413161,22417920 22405076,22408287,22413041,22413359,22418010 nan CDC42 nan nan 0,0,0,0,0 -4352 MPL;NM_005373.3 1 + 43803519 43818443 43803519 43818443 12 43803519,43803769,43804212,43804941,43805634,43806057,43812115,43812462,43814513,43814933,43817886,43818188 43803598,43803902,43804391,43805240,43805797,43806184,43812300,43812605,43814673,43815030,43817974,43818443 nan MPL nan nan 0,0,0,0,0,0,0,0,0,0,0,0 -9939 RBM8A;NM_005105.5 1 + 145507666 145509211 145507666 145509211 6 145507666,145508015,145508206,145508474,145508915,145509165 145507733,145508075,145508284,145508611,145509052,145509211 nan RBM8A nan nan 0,0,0,0,0,0 -2629 GBA;NM_000157.4 1 - 155204785 155210903 155204785 155210903 11 155204785,155204985,155205471,155206035,155207131,155207924,155208307,155209406,155209676,155210420,155210876 155204891,155205102,155205635,155206260,155207369,155208097,155208441,155209553,155209868,155210508,155210903 nan GBA nan nan 0,0,0,0,0,0,0,0,0,0,0 -2153 F5;NM_000130.5 1 - 169483550 169555624 169483550 169555624 25 169483550,169484681,169487649,169489757,169492434,169493038,169494074,169495138,169497152,169498845,169500023,169505743,169509531,169513533,169515679,169519038,169519877,169521794,169524419,169525883,169528390,169529791,169541458,169551668,169555466 169483697,169484864,169487801,169489902,169492590,169493142,169494146,169495255,169497332,169499056,169500260,169505918,169512352,169513746,169515830,169519253,169519977,169521972,169524585,169526105,169528534,169530004,169541581,169551760,169555624 nan F5 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -5321 PLA2G4A;NM_024420.3 1 + 186823486 186957640 186823486 186957640 17 186823486,186839566,186862142,186863229,186876096,186880379,186901894,186908139,186909111,186915768,186916000,186919788,186925233,186934540,186946724,186948446,186957508 186823519,186839648,186862291,186863343,186876134,186880521,186902031,186908362,186909226,186915906,186916093,186919860,186925476,186934725,186946920,186948604,186957640 nan PLA2G4A nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2165 F13B;NM_001994.3 1 - 197008507 197036353 197008507 197036353 12 197008507,197009651,197019826,197021763,197024844,197026142,197026415,197029495,197030028,197030913,197031986,197036289 197008541,197009865,197020009,197021964,197025027,197026328,197026595,197029672,197030205,197031099,197032187,197036353 nan F13B nan nan 0,0,0,0,0,0,0,0,0,0,0,0 -1130 LYST;NM_000081.4 1 - 235826239 235993717 235826239 235993717 51 235826239,235827283,235827764,235840390,235840779,235850248,235856649,235860382,235866046,235872390,235875356,235878500,235880011,235883960,235887327,235891375,235892895,235894146,235894331,235896802,235897129,235897782,235904721,235907278,235909635,235914509,235915304,235916343,235918777,235920580,235922271,235926019,235929378,235933459,235937141,235938212,235940362,235944164,235945226,235950499,235952000,235954998,235956802,235963619,235964170,235966207,235967803,235969042,235971754,235976270,235993525 235826378,235827355,235827921,235840488,235840919,235850347,235856786,235860572,235866277,235872608,235875497,235878657,235880078,235884205,235887480,235891431,235892957,235894243,235894477,235896991,235897206,235897959,235904928,235907457,235909827,235914662,235915471,235916574,235918947,235920758,235922899,235926151,235929577,235933597,235937291,235938386,235940608,235944355,235945387,235950673,235952145,235955425,235956912,235963686,235964397,235966364,235967965,235970072,235973834,235976361,235993717 nan LYST nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -64240 ABCG5;NM_022436.3 2 - 44040254 44065818 44040254 44065818 13 44040254,44041615,44047053,44049935,44051051,44051357,44052027,44053520,44055121,44058907,44059085,44064972,44065675 44040448,44041728,44047239,44050074,44051257,44051571,44052157,44053660,44055254,44059006,44059222,44065094,44065818 nan ABCG5 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 -64241 ABCG8;NM_022437.3 2 + 44066192 44105052 44066192 44105052 13 44066192,44071645,44073293,44078722,44079492,44079737,44099114,44099361,44100925,44101545,44102284,44104699,44104914 44066255,44071747,44073450,44078961,44079625,44080007,44099277,44099445,44101125,44101622,44102552,44104827,44105052 nan ABCG8 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 -90411 MCFD2;NM_139279.6 2 - 47132601 47136310 47132601 47136310 3 47132601,47134948,47136161 47132733,47135108,47136310 nan MCFD2 nan nan 0,0,0 -2677 GGCX;NM_000821.7 2 - 85777056 85788551 85777056 85788551 15 85777056,85777677,85778047,85778602,85778934,85779538,85780061,85780354,85781265,85782606,85783304,85785562,85786039,85787937,85788508 85777249,85777873,85778195,85778733,85779104,85779690,85780193,85780620,85781429,85782713,85783383,85785728,85786198,85788108,85788551 nan GGCX nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -1281 COL3A1;NM_000090.4 2 + 189839215 189876500 189839215 189876500 51 189839215,189849485,189849922,189850390,189851784,189852806,189853315,189854121,189854821,189855032,189855729,189856212,189856394,189856909,189857612,189858086,189858763,189858959,189859266,189859449,189859771,189860417,189860850,189861123,189861890,189862061,189862425,189862991,189863399,189864010,189864195,189864567,189866122,189866261,189867023,189867680,189868136,189868459,189868707,189868982,189870075,189870931,189871070,189871662,189872225,189872610,189872760,189873649,189874903,189875373,189876353 189839294,189849688,189849973,189850504,189851865,189852860,189853369,189854175,189854875,189855086,189855783,189856257,189856448,189856954,189857666,189858185,189858808,189859058,189859320,189859557,189859825,189860516,189860904,189861222,189861944,189862115,189862479,189863045,189863444,189864109,189864303,189864621,189866176,189866315,189867077,189867788,189868190,189868513,189868869,189869090,189870183,189870985,189871178,189871716,189872333,189872664,189872868,189873947,189875091,189875616,189876500 nan COL3A1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -23218 NBEAL2;NM_015175.3 3 + 47021351 47050810 47021351 47050810 54 47021351,47030158,47030331,47030574,47030749,47031000,47032708,47032895,47033329,47033964,47035426,47035944,47036521,47037203,47037421,47037760,47038240,47038443,47038748,47039050,47039556,47039952,47040206,47040448,47040804,47041119,47041378,47042490,47042768,47043178,47043409,47043860,47044134,47044446,47044663,47045305,47045566,47045984,47046461,47046670,47046978,47047227,47047435,47047654,47047822,47048555,47048730,47049014,47049305,47049559,47049772,47050009,47050478,47050708 47021402,47030247,47030460,47030656,47030871,47031083,47032794,47033178,47033436,47034045,47035510,47036043,47037123,47037336,47037541,47038082,47038323,47038536,47038923,47039184,47039716,47040055,47040369,47040607,47040964,47041205,47041894,47042669,47042928,47043316,47043778,47044010,47044292,47044571,47044799,47045466,47045883,47046080,47046586,47046811,47047109,47047337,47047553,47047752,47047939,47048645,47048840,47049187,47049400,47049676,47049931,47050158,47050614,47050810 nan NBEAL2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2815 GP9;NM_000174.5 3 + 128780582 128781116 128780582 128781116 1 128780582 128781116 nan GP9 nan nan 0 -84343 HPS3;NM_032383.5 3 + 148847510 148890009 148847510 148890009 17 148847510,148857790,148858803,148859081,148863140,148868385,148871280,148872893,148875136,148876452,148877832,148879934,148880476,148881628,148884820,148885679,148889881 148847727,148858285,148858975,148859167,148863333,148868467,148871435,148873002,148875318,148876633,148878066,148880120,148880665,148881736,148885027,148885770,148890009 nan HPS3 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -64805 P2RY12;NM_022788.5 3 - 151055604 151056633 151055604 151056633 1 151055604 151056633 nan P2RY12 nan nan 0 -2122 MECOM;NM_004991.4 3 - 168802696 169381160 168802696 169381160 17 168802696,168806787,168807787,168810745,168812863,168818672,168819847,168825713,168830574,168833170,168838843,168840367,168845631,168849216,168861485,169098974,169381123 168802831,168806971,168808024,168810890,168813033,168818750,168820014,168825740,168830662,168834527,168838997,168840515,168845848,168849319,168861620,169099312,169381160 nan MECOM nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -7066 THPO;NM_000460.4 3 - 184090300 184094047 184090300 184094047 5 184090300,184091202,184093302,184093675,184094034 184090966,184091370,184093389,184093803,184094047 nan THPO nan nan 0,0,0,0,0 -3827 KNG1;NM_001102416.3 3 + 186435331 186460120 186435331 186460120 10 186435331,186437893,186440225,186442876,186445025,186449333,186450290,186456887,186457116,186459310 186435526,186438004,186440310,186443049,186445133,186449418,186450463,186456995,186457203,186460120 nan KNG1 nan nan 0,0,0,0,0,0,0,0,0,0 -2244 FGB;NM_005141.5 4 + 155484170 155491802 155484170 155491802 8 155484170,155486959,155487640,155488744,155489532,155490333,155490665,155491570 155484284,155487151,155487824,155488972,155489646,155490459,155490951,155491802 nan FGB nan nan 0,0,0,0,0,0,0,0 -2243 FGA;NM_000508.5 4 - 155505275 155511839 155505275 155511839 6 155505275,155506689,155508663,155509944,155510588,155511785 155505985,155508070,155508809,155510128,155510714,155511839 nan FGA nan nan 0,0,0,0,0,0 -2266 FGG;NM_021870.3 4 - 155525985 155533761 155525985 155533761 9 155525985,155527856,155529617,155530781,155531218,155532956,155533169,155533542,155533683 155526218,155528134,155529802,155530915,155531349,155533050,155533353,155533587,155533761 nan FGG nan nan 0,0,0,0,0,0,0,0,0 -3818 KLKB1;NM_000892.5 4 + 187149349 187179366 187149349 187179366 14 187149349,187153280,187155105,187157934,187159409,187171396,187172372,187172640,187172902,187173170,187175741,187177145,187178379,187179174 187149407,187153443,187155212,187158094,187159519,187171556,187172482,187172803,187173015,187173339,187175917,187177241,187178519,187179366 nan KLKB1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2160 F11;NM_000128.4 4 + 187188290 187209768 187188290 187209768 14 187188290,187192762,187194224,187195269,187196940,187197384,187201165,187201376,187201627,187205245,187206791,187207568,187208837,187209606 187188345,187192925,187194331,187195429,187197050,187197544,187201275,187201539,187201734,187205414,187206967,187207664,187208977,187209768 nan F11 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2533 FYB1;NM_001465.6 5 - 39107544 39203062 39107544 39203062 18 39107544,39108332,39110457,39118975,39119636,39122437,39124354,39126099,39127842,39130691,39134309,39134956,39137701,39138758,39139334,39141196,39153549,39201927 39107567,39108364,39110491,39119138,39119736,39122504,39124380,39126237,39127909,39130714,39134451,39135116,39137822,39138793,39139354,39141243,39153706,39203062 nan FYB1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -8546 AP3B1;NM_003664.5 5 - 77298725 77590403 77298725 77590403 27 77298725,77311233,77316515,77330184,77334866,77385216,77396776,77406030,77409575,77411949,77423853,77424944,77436966,77452081,77458642,77461433,77471449,77471607,77473162,77477330,77511878,77521365,77523195,77523967,77536685,77563343,77590275 77298879,77311372,77316613,77330269,77335098,77385323,77396849,77406178,77409747,77412058,77423984,77425131,77437143,77452191,77458775,77461496,77471521,77471662,77473260,77477486,77512061,77521432,77523356,77524063,77536760,77563419,77590403 nan AP3B1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -1729 DIAPH1;NM_005219.5 5 - 140896417 140998481 140896417 140998481 28 140896417,140903709,140905604,140905863,140907139,140908019,140908268,140908738,140909169,140913901,140915620,140951492,140953058,140954533,140955796,140956322,140957041,140957791,140958081,140958654,140960310,140961878,140962772,140963051,140963690,140966608,140967790,140998364 140896575,140903796,140905740,140906028,140907264,140908149,140908508,140908840,140909264,140914000,140915629,140951607,140953775,140954713,140955861,140956438,140957158,140957910,140958192,140958763,140960450,140961942,140962859,140963182,140963792,140966764,140967817,140998481 nan DIAPH1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2161 F12;NM_000505.4 5 - 176829292 176836528 176829292 176836528 14 176829292,176829550,176830254,176830481,176830859,176831196,176831499,176831810,176832054,176832323,176832735,176832962,176836046,176836471 176829460,176829699,176830398,176830618,176831091,176831414,176831665,176831915,176832186,176832434,176832806,176833062,176836104,176836528 nan F12 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2162 F13A1;NM_000129.4 6 - 6145851 6318897 6145851 6318897 14 6145851,6152045,6167690,6174812,6182220,6196029,6197455,6222265,6224918,6248544,6251043,6266790,6305583,6318767 6146005,6152182,6167851,6175100,6182374,6196118,6197559,6222404,6225093,6248652,6251162,6267042,6305772,6318897 nan F13A1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 -84062 DTNBP1;NM_032122.5 6 - 15523205 15663100 15523205 15663100 10 15523205,15524756,15533470,15593289,15615497,15627573,15637974,15651543,15652317,15663044 15523450,15524900,15533626,15593312,15615630,15627706,15638035,15651594,15652371,15663100 nan DTNBP1 nan nan 0,0,0,0,0,0,0,0,0,0 -80739 MPIG6B;NM_138272.3 6 + 31691160 31692851 31691160 31692851 6 31691160,31691415,31691918,31692363,31692541,31692746 31691221,31691763,31692009,31692404,31692621,31692851 nan MPIG6B nan nan 0,0,0,0,0,0 -7148 TNXB;NM_019105.8 6 - 32009125 32065975 32009125 32065975 43 32009125,32009547,32009788,32010042,32010231,32010475,32010727,32010951,32011213,32011525,32011783,32012157,32012782,32013951,32015510,32016139,32017046,32017774,32020446,32021164,32023627,32024362,32025834,32029173,32029933,32032597,32035437,32036166,32036598,32037329,32037903,32039766,32041423,32046809,32049144,32049812,32052189,32053526,32056561,32056999,32062852,32063387,32065572 32009227,32009711,32009950,32010139,32010383,32010608,32010858,32011095,32011333,32011669,32011906,32012493,32013103,32014233,32015789,32016427,32017364,32018098,32020770,32021482,32023951,32024680,32026167,32029497,32030260,32032894,32035761,32036484,32036913,32037638,32038191,32040075,32041729,32047142,32049450,32050103,32052486,32053895,32056825,32057156,32062968,32065226,32065975 nan TNXB nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -60 ACTB;NM_001101.5 7 - 5567378 5569288 5567378 5569288 5 5567378,5567634,5567911,5568791,5569165 5567522,5567816,5568350,5569031,5569288 nan ACTB nan nan 0,0,0,0,0 -54205 CYCS;NM_018947.6 7 - 25163319 25163738 25163319 25163738 2 25163319,25163569 25163468,25163738 nan CYCS nan nan 0,0 -10095 ARPC1B;NM_005720.4 7 + 98983337 98992112 98983337 98992112 9 98983337,98984307,98985661,98987527,98988515,98988800,98990293,98991651,98992073 98983401,98984412,98985884,98987635,98988722,98988876,98990499,98991742,98992112 nan ARPC1B nan nan 0,0,0,0,0,0,0,0,0 -5054 SERPINE1;NM_000602.5 7 + 100771674 100780723 100771674 100780723 8 100771674,100773701,100775155,100776975,100778774,100778995,100780281,100780685 100771945,100773935,100775350,100777174,100778875,100779082,100780365,100780723 nan SERPINE1 nan nan 0,0,0,0,0,0,0,0 -6916 TBXAS1;NM_001061.7 7 + 139529189 139719899 139529189 139719899 13 139529189,139572033,139575383,139611023,139635989,139653166,139655257,139657432,139661717,139706890,139715522,139717470,139719824 139529278,139572127,139575436,139611120,139636106,139653255,139655406,139657563,139662032,139706982,139715660,139717633,139719899 nan TBXAS1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 -10020 GNE;NM_005476.7 9 - 36217361 36249352 36217361 36249352 11 36217361,36218179,36219834,36222773,36223369,36227244,36229017,36233916,36236828,36246027,36249188 36217597,36218296,36220017,36222995,36223499,36227455,36229105,36234129,36236981,36246479,36249352 nan GNE nan nan 0,0,0,0,0,0,0,0,0,0,0 -5742 PTGS1;NM_000962.4 9 + 125133363 125154823 125133363 125154823 11 125133363,125133464,125140177,125140711,125141053,125143649,125143942,125145787,125148724,125152476,125154467 125133370,125133551,125140294,125140852,125141197,125143831,125144026,125146034,125149011,125152624,125154823 nan PTGS1 nan nan 0,0,0,0,0,0,0,0,0,0,0 -2022 ENG;NM_001114753.3 9 - 130577960 130616634 130577960 130616634 15 130577960,130578221,130579427,130580398,130580994,130581900,130582178,130586582,130587078,130587509,130587973,130588788,130591965,130605372,130616567 130578085,130578332,130579482,130580656,130581111,130581939,130582316,130586725,130587253,130587636,130588139,130588951,130592106,130605524,130616634 nan ENG nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -8328 GFI1B;NM_004188.8 9 + 135862065 135866437 135862065 135866437 6 135862065,135862668,135863583,135864447,135865128,135866258 135862165,135862806,135863855,135864585,135865294,135866437 nan GFI1B nan nan 0,0,0,0,0,0 -22852 ANKRD26;NM_001256053.2 10 - 27294518 27389255 27294518 27389255 34 27294518,27295845,27301810,27303422,27306430,27311486,27313375,27317780,27318214,27322153,27323724,27326114,27326799,27328893,27332354,27333085,27335281,27337729,27342248,27349273,27349440,27350072,27352916,27355415,27356085,27366266,27366561,27368017,27371731,27375467,27381334,27382277,27382613,27389013 27294652,27295891,27302039,27303640,27306721,27311616,27313488,27317874,27318285,27322306,27324681,27326252,27326983,27329107,27332496,27333119,27335449,27337908,27342319,27349346,27349469,27350171,27353010,27355477,27356215,27366469,27366622,27368090,27371762,27375538,27381441,27382451,27382728,27389255 nan ANKRD26 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -5328 PLAU;NM_002658.6 10 + 75671313 75676323 75671313 75676323 10 75671313,75671798,75671972,75672681,75673047,75673296,75673737,75674533,75675008,75676146 75671370,75671826,75672080,75672856,75673139,75673516,75673886,75674674,75675157,75676323 nan PLAU nan nan 0,0,0,0,0,0,0,0,0,0 -3257 HPS1;NM_000195.5 10 - 100177320 100202997 100177320 100202997 18 100177320,100177931,100179801,100182125,100183359,100183509,100184069,100185297,100185574,100186971,100189329,100189547,100190327,100190887,100193739,100195028,100195391,100202880 100177483,100178014,100179915,100182270,100183425,100183644,100184131,100185477,100185742,100187021,100189399,100189646,100190427,100191048,100193848,100195171,100195529,100202997 nan HPS1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -79803 HPS6;NM_024747.6 10 + 103825231 103827559 103825231 103827559 1 103825231 103827559 nan HPS6 nan nan 0 -64376 IKZF5;NM_001271840.1 10 - 124753295 124758141 124753295 124758141 3 124753295,124755509,124758008 124754239,124755692,124758141 nan IKZF5 nan nan 0,0,0 -6786 STIM1;NM_003156.4 11 + 3877500 4113028 3877500 4113028 12 3877500,3988781,4045102,4076755,4080510,4091255,4095731,4103413,4104111,4104492,4107706,4112511 3877639,3988912,4045217,4076867,4080626,4091433,4095909,4103581,4104212,4104728,4107773,4113028 nan STIM1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0 -11234 HPS5;NM_181507.2 11 - 18301428 18339405 18301428 18339405 22 18301428,18303496,18305341,18306892,18308137,18309081,18309439,18312988,18314445,18316566,18317545,18318344,18319105,18320338,18322374,18326968,18327681,18330492,18332287,18332933,18333460,18339297 18301489,18303767,18305448,18307006,18308257,18309237,18309560,18313566,18314523,18316716,18317669,18318531,18319264,18320517,18322463,18327040,18327894,18330626,18332480,18332998,18333571,18339405 nan HPS5 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2147 F2;NM_000506.5 11 + 46740785 46760958 46740785 46760958 14 46740785,46741251,46742072,46742339,46744729,46744931,46747408,46748047,46748260,46749545,46750213,46750929,46760597,46760814 46740864,46741412,46742097,46742390,46744835,46745068,46747723,46748176,46748387,46749713,46750387,46751111,46760668,46760958 nan F2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 -83706 FERMT3;NM_031471.6 11 + 63974836 63990964 63974836 63990964 14 63974836,63978082,63978523,63978746,63979116,63986722,63986995,63987211,63987362,63987691,63987907,63988487,63990519,63990784 63974996,63978316,63978643,63978915,63979219,63986830,63987130,63987261,63987487,63987798,63988141,63988612,63990661,63990964 nan FERMT3 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0 -10235 RASGRP2;NM_153819.1 11 - 64494773 64510338 64494773 64510338 15 64494773,64496334,64497233,64497524,64502583,64503013,64503374,64504224,64506831,64507107,64507484,64508419,64508910,64509481,64510265 64494832,64496514,64497270,64497666,64502699,64503136,64503452,64504506,64506948,64507281,64507635,64508551,64508973,64509584,64510338 nan RASGRP2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2313 FLI1;NM_002017.5 11 + 128564153 128680883 128564153 128680883 9 128564153,128628009,128638012,128642676,128651852,128675260,128677074,128679051,128680353 128564171,128628221,128638167,128642880,128651918,128675326,128677134,128679099,128680883 nan FLI1 nan nan 0,0,0,0,0,0,0,0,0 -7450 VWF;NM_000552.5 12 - 6058180 6232362 6058180 6232362 51 6058180,6058951,6061009,6061556,6062661,6076651,6077292,6078376,6080764,6085276,6090951,6092315,6094210,6094728,6100984,6103027,6103580,6105167,6120782,6121252,6122646,6125254,6125681,6125919,6127530,6131065,6131905,6132796,6134745,6135071,6138507,6140609,6143853,6145553,6153456,6155888,6161708,6166022,6167014,6172119,6173411,6174302,6180462,6181496,6182784,6184500,6204625,6219539,6220031,6230339,6232307 6058369,6059049,6061049,6061685,6062760,6076768,6077333,6078557,6080875,6085426,6091157,6092420,6094285,6094831,6101184,6103369,6103773,6105388,6120960,6121296,6122811,6125398,6125822,6126036,6128909,6131201,6132064,6132953,6134859,6135212,6138654,6140744,6143992,6145657,6153617,6155983,6161949,6166238,6167210,6172220,6173550,6174439,6180509,6181608,6182907,6184717,6204750,6219748,6220134,6230504,6232362 nan VWF nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -2120 ETV6;NM_001987.5 12 + 11803061 12043980 11803061 12043980 8 11803061,11905383,11992073,12006360,12022357,12037378,12038859,12043874 11803094,11905513,11992238,12006495,12022903,12037521,12038960,12043980 nan ETV6 nan nan 0,0,0,0,0,0,0,0 -196527 ANO6;NM_001025356.3 12 + 45610104 45823094 45610104 45823094 20 45610104,45695796,45725077,45740804,45741810,45742300,45744441,45751072,45761470,45771835,45781943,45784203,45795577,45796854,45797221,45803139,45810481,45814853,45816739,45822887 45610174,45695876,45725206,45740870,45742098,45742414,45744557,45751207,45761576,45771896,45782086,45784281,45795803,45797024,45797319,45803270,45810687,45815056,45816845,45823094 nan ANO6 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -94 ACVRL1;NM_001077401.2 12 + 52306258 52314677 52306258 52314677 9 52306258,52306882,52307342,52307757,52308222,52309008,52309819,52312768,52314542 52306319,52307134,52307554,52307857,52308369,52309284,52310017,52312899,52314677 nan ACVRL1 nan nan 0,0,0,0,0,0,0,0,0 -2155 F7;NM_000131.4 13 + 113760155 113773322 113760155 113773322 9 113760155,113761158,113765003,113768065,113768160,113769973,113771079,113771786,113772726 113760219,113761224,113765164,113768090,113768274,113770114,113771189,113771910,113773322 nan F7 nan nan 0,0,0,0,0,0,0,0,0 -2159 F10;NM_000504.4 13 + 113777169 113803831 113777169 113803831 8 113777169,113783765,113792770,113793670,113795232,113798164,113801692,113803229 113777239,113783926,113792795,113793784,113795364,113798409,113801810,113803831 nan F10 nan nan 0,0,0,0,0,0,0,0 -87 ACTN1;NM_001102.4 14 - 69341575 69445773 69341575 69445773 21 69341575,69343798,69345705,69346678,69347526,69349174,69349589,69350884,69351491,69352141,69356855,69358769,69360371,69369193,69371371,69376034,69376671,69378872,69387722,69392274,69445668 69341734,69343957,69345786,69346825,69347706,69349309,69349772,69351025,69351600,69352292,69357003,69359000,69360464,69369279,69371453,69376113,69376759,69378959,69387842,69392389,69445773 nan ACTN1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -63894 VIPAS39;NM_022067.4 14 - 77893958 77920445 77893958 77920445 19 77893958,77894712,77895348,77896023,77900184,77900604,77901601,77902186,77904150,77907408,77908902,77909461,77910591,77914836,77915635,77916056,77917529,77919641,77920352 77893979,77894817,77895438,77896110,77900274,77900646,77901736,77902262,77904224,77907436,77909005,77909495,77910684,77914893,77915700,77916095,77917676,77919744,77920445 nan VIPAS39 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -113189 CHST14;NM_130468.4 15 + 40763412 40764543 40763412 40764543 1 40763412 40764543 nan CHST14 nan nan 0 -26258 BLOC1S6;NM_012388.4 15 + 45879641 45898712 45879641 45898712 5 45879641,45884332,45895297,45897625,45898592 45879723,45884474,45895385,45897712,45898712 nan BLOC1S6 nan nan 0,0,0,0,0 -26276 VPS33B;NM_018668.5 15 - 91542204 91565479 91542204 91565479 23 91542204,91542906,91543129,91543719,91544618,91545279,91546314,91548106,91548284,91548609,91548923,91549202,91549601,91549881,91550179,91550698,91551099,91553030,91557033,91557613,91560192,91561034,91565383 91542284,91543023,91543205,91543821,91544692,91545412,91546361,91548161,91548349,91548684,91549014,91549289,91549675,91549959,91550276,91550803,91551194,91553076,91557101,91557663,91560254,91561115,91565479 nan VPS33B nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -79001 VKORC1;NM_024006.6 16 - 31102454 31106050 31102454 31106050 3 31102454,31104632,31105877 31102663,31104742,31106050 nan VKORC1 nan nan 0,0,0 -5345 SERPINF2;NM_000934.4 17 + 1648289 1657828 1648289 1657828 9 1648289,1648468,1648626,1649001,1650312,1650602,1651891,1655879,1657415 1648352,1648507,1648689,1649203,1650456,1650806,1652034,1656084,1657828 nan SERPINF2 nan nan 0,0,0,0,0,0,0,0,0 -2811 GP1BA;NM_000173.7 17 + 4835899 4837858 4835899 4837858 1 4835899 4837858 nan GP1BA nan nan 0 -342618 SLFN14;NM_001129820.2 17 - 33875257 33885081 33875257 33885081 4 33875257,33879748,33881594,33884021 33876092,33880463,33881723,33885081 nan SLFN14 nan nan 0,0,0,0 -3674 ITGA2B;NM_000419.5 17 - 42449731 42466841 42449731 42466841 30 42449731,42451721,42452026,42452365,42452958,42453200,42453452,42453675,42454376,42455065,42455729,42456010,42457056,42457369,42457613,42457753,42457967,42458246,42460860,42461261,42461452,42461678,42461905,42462315,42462531,42462653,42462918,42463191,42463377,42466653 42449791,42451838,42452128,42452479,42453084,42453353,42453552,42453756,42454456,42455158,42455877,42456078,42457182,42457521,42457669,42457858,42458013,42458429,42461072,42461314,42461506,42461722,42461953,42462444,42462577,42462703,42463084,42463289,42463499,42466841 nan ITGA2B nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -3690 ITGB3;NM_000212.3 17 + 45331227 45387570 45331227 45387570 15 45331227,45351784,45360719,45361808,45363625,45364435,45367046,45367550,45368319,45369504,45376673,45377843,45380086,45384836,45387504 45331306,45351870,45360915,45362061,45363788,45364597,45367142,45367640,45368454,45369934,45376896,45377944,45380206,45385003,45387570 nan ITGB3 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -3998 LMAN1;NM_005570.4 18 - 56998324 57026476 56998324 57026476 13 56998324,56998649,57000322,57005788,57005991,57013150,57014744,57016344,57020433,57021750,57022544,57022735,57026262 56998361,56998771,57000476,57005859,57006185,57013283,57014803,57016468,57020533,57021812,57022652,57022890,57026476 nan LMAN1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 -2531 KDSR;NM_002035.4 18 - 60999014 61034351 60999014 61034351 10 60999014,61002489,61006032,61011642,61018120,61022436,61022730,61026968,61030011,61034243 60999134,61002591,61006116,61011726,61018312,61022532,61022796,61027025,61030101,61034351 nan KDSR nan nan 0,0,0,0,0,0,0,0,0,0 -8943 AP3D1;NM_003938.8 19 - 2102171 2151333 2102171 2151333 30 2102171,2108685,2109084,2109871,2110134,2110705,2111283,2111677,2114123,2114746,2115217,2115536,2116205,2116603,2117220,2118599,2120860,2121161,2121732,2123356,2123828,2127150,2129088,2129316,2130406,2132469,2137009,2137725,2138617,2151237 2102267,2108765,2109206,2109957,2110223,2110895,2111331,2111827,2114301,2114820,2115417,2115612,2116277,2116745,2117366,2118831,2121091,2121310,2121878,2123405,2123878,2127200,2129162,2129456,2130536,2132577,2137090,2137806,2138713,2151333 nan AP3D1 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -6915 TBXA2R;NM_001060.6 19 - 3595685 3600632 3595685 3600632 2 3595685,3599846 3595931,3600632 nan TBXA2R nan nan 0,0 -6813 STXBP2;NM_006949.4 19 + 7702035 7712696 7702035 7712696 19 7702035,7703611,7703904,7704616,7705616,7705785,7706590,7706919,7707088,7707314,7707651,7707868,7708050,7709499,7710082,7711134,7712047,7712239,7712610 7702072,7703661,7703986,7704693,7705695,7705889,7706739,7707004,7707219,7707422,7707709,7707934,7708131,7709638,7710192,7711230,7712133,7712397,7712696 nan STXBP2 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -7171 TPM4;NM_003290.3 19 + 16187375 16212156 16187375 16212156 8 16187375,16192722,16197232,16198836,16199854,16204345,16204493,16212073 16187507,16192856,16197350,16198907,16199930,16204408,16204563,16212156 nan TPM4 nan nan 0,0,0,0,0,0,0,0 -388552 BLOC1S3;NM_212550.5 19 + 45682554 45683163 45682554 45683163 1 45682554 45683163 nan BLOC1S3 nan nan 0 -51206 GP6;NM_001083899.2 19 - 55525449 55549604 55525449 55549604 8 55525449,55527046,55530019,55536585,55538945,55543506,55543873,55549570 55526533,55527101,55530079,55536639,55539230,55543764,55543906,55549604 nan GP6 nan nan 0,0,0,0,0,0,0,0 -7056 THBD;NM_000361.3 20 - 23028413 23030141 23028413 23030141 1 23028413 23030141 nan THBD nan nan 0 -6714 SRC;NM_005417.4 20 + 36012556 36031782 36012556 36031782 11 36012556,36014477,36022297,36022576,36024564,36026101,36028517,36030004,36030837,36031151,36031573 36012806,36014577,36022396,36022680,36024714,36026257,36028697,36030081,36030991,36031283,36031782 nan SRC nan nan 0,0,0,0,0,0,0,0,0,0,0 -81027 TUBB1;NM_030773.4 20 + 57594577 57599838 57594577 57599838 4 57594577,57597899,57598544,57598759 57594634,57598008,57598655,57599838 nan TUBB1 nan nan 0,0,0,0 -861 RUNX1;NM_001754.5 21 - 36164431 36421196 36164431 36421196 8 36164431,36171597,36206706,36231770,36252853,36259139,36265221,36421138 36164907,36171759,36206898,36231875,36253010,36259393,36265260,36421196 nan RUNX1 nan nan 0,0,0,0,0,0,0,0 -2812 GP1BB;NM_000407.5 22 + 19711092 19711987 19711092 19711987 2 19711092,19711376 19711102,19711987 nan GP1BB nan nan 0,0 -89781 HPS4;NM_022081.6 22 - 26849198 26877728 26849198 26877728 13 26849198,26853824,26854410,26859882,26861420,26862191,26864516,26866684,26868267,26868797,26872958,26875230,26877687 26849370,26853933,26854543,26860792,26861517,26862228,26864589,26866779,26868384,26868905,26873102,26875321,26877728 nan HPS4 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0 -4627 MYH9;NM_002473.6 22 - 36678713 36745281 36678713 36745281 40 36678713,36680138,36680448,36681166,36681703,36681910,36682763,36684297,36684772,36685130,36688031,36689374,36689804,36690137,36690977,36691550,36692888,36694964,36696172,36696896,36697579,36698613,36700040,36701078,36701975,36702459,36705326,36708093,36710189,36712561,36714251,36715584,36716264,36716842,36717802,36718473,36722612,36723505,36737414,36744948 36678831,36680311,36680557,36681375,36681827,36681999,36682892,36684459,36684985,36685343,36688280,36689527,36689909,36690344,36691122,36691763,36693060,36695088,36696310,36697103,36697711,36698722,36700201,36701148,36702097,36702653,36705441,36708267,36710363,36712714,36714370,36715680,36716408,36716941,36717866,36718566,36722706,36723533,36737571,36745281 nan MYH9 nan nan 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 -7454 WAS;NM_000377.3 X + 48542242 48549553 48542242 48549553 12 48542242,48542671,48543935,48544122,48544334,48544469,48545169,48546442,48546688,48547048,48547708,48549497 48542374,48542812,48544022,48544225,48544376,48544523,48545344,48546485,48546842,48547455,48547823,48549553 nan WAS nan nan 0,0,0,0,0,0,0,0,0,0,0,0 -2623 GATA1;NM_002049.4 X + 48649516 48652571 48649516 48652571 5 48649516,48650250,48650729,48651578,48652199 48649736,48650628,48650875,48651704,48652571 nan GATA1 nan nan 0,0,0,0,0 -2158 F9;NM_000133.4 X + 138612923 138644230 138612923 138644230 8 138612923,138619168,138619520,138623234,138630521,138633220,138642899,138643682 138613011,138619332,138619545,138623348,138630650,138633423,138643014,138644230 nan F9 nan nan 0,0,0,0,0,0,0,0 -2316 FLNA;NM_001456.3 X - 153577216 153599613 153577216 153599613 46 153577216,153577729,153578016,153578398,153579276,153579948,153580251,153580548,153580920,153581139,153581368,153581663,153581921,153582282,153582518,153582748,153582983,153583192,153585801,153586566,153586812,153587351,153587613,153587851,153588099,153588357,153589675,153590037,153590346,153590609,153590785,153591028,153592389,153592626,153592893,153593188,153593503,153593716,153594391,153594675,153594929,153595099,153595764,153596008,153596209,153599240 153577404,153577933,153578235,153578575,153579409,153580064,153580389,153580815,153581043,153581292,153581572,153581825,153582095,153582411,153582659,153582851,153583079,153583440,153585991,153586723,153586936,153587522,153587774,153588014,153588273,153588955,153589938,153590155,153590516,153590700,153590946,153591152,153592533,153592740,153593087,153593325,153593627,153593854,153594592,153594838,153595007,153595218,153595912,153596106,153596458,153599613 nan FLNA nan nan 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F8;NM_000132.4 2157 -X 154197605 154197827 X-154197605-154197827 0 + F8;NM_000132.4 2157 -X 154212961 154213078 X-154212961-154213078 0 + F8;NM_000132.4 2157 -X 154215511 154215580 X-154215511-154215580 0 + F8;NM_000132.4 2157 -X 154221210 154221423 X-154221210-154221423 0 + F8;NM_000132.4 2157 -X 154225247 154225370 X-154225247-154225370 0 + F8;NM_000132.4 2157 -X 154227753 154227875 X-154227753-154227875 0 + F8;NM_000132.4 2157 -X 154250684 154250827 X-154250684-154250827 0 + F8;NM_000132.4 2157 From 102c667632ca3ea79a2f578738f68f00e792e583 Mon Sep 17 00:00:00 2001 From: natashapinto Date: Mon, 8 Apr 2024 11:03:38 +0100 Subject: [PATCH 11/11] testing statement --- LiveBedfiles/Pan5223_LogFile.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/LiveBedfiles/Pan5223_LogFile.md b/LiveBedfiles/Pan5223_LogFile.md index a1f180e0..18618b7a 100644 --- a/LiveBedfiles/Pan5223_LogFile.md +++ b/LiveBedfiles/Pan5223_LogFile.md @@ -44,4 +44,7 @@ cut -f 1-4 Pan5223data.bed > Pan5223data_4col.bed; rm Pan5223data.bed; mv Pan522 git mv Pan5223data.bed Pan5223_CNV.bed ## Delete unrequired files -git rm Pan5223dataSambamba.bed Pan5223dataRefSeqFormat.txt \ No newline at end of file +git rm Pan5223dataSambamba.bed Pan5223dataRefSeqFormat.txt + +## Testing +Pan5223_CNV.bed was tested using DNANexus app ED_cnv_calling_v1.3.0 in 003_240223_exomedepth_bedfiles. The app completed sucessfully. \ No newline at end of file