From 5ef115943848159951a2c9e53f8af06be4794a32 Mon Sep 17 00:00:00 2001 From: Ryan Layer Date: Wed, 9 Apr 2014 10:46:56 -0400 Subject: [PATCH] Update README.rst Update options and add a note about trimming. --- README.rst | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/README.rst b/README.rst index f1cfed2..c4c8975 100644 --- a/README.rst +++ b/README.rst @@ -103,7 +103,7 @@ Usage General options :: - -e Show evidence for each call + -e The default output reports the predicted breakpoint. This option includes the evidence supporting each call. @@ -119,6 +119,13 @@ set. The sum of weights in the evidence set must be above this value. Each predicted breakpoint interval has a probability array associated with it. The intervals can be trimmed of values that are below some trimming percentile. +NOTE: We recommend "-tt 0.0" (no trimming) since LUMPY now reports both the 95% +confidence interval and the most probable single base for each breakpoint. +:: + + -P + +Print the breakpoint probability array. :: -x excluded regions bed file @@ -273,10 +280,12 @@ Tab separated:: 11. type 12. id of samples containing evidence for this breakpoint 13. strand configurations observed in the evidence set + 14. point within the two breakpoint with the maximum probability + 15. segmetn of each breakpoint that contains 95% of the probability Example:: - chr1 34971904 34971945 chr1 34976002 34976043 0x7f9eb0917210 0.0110386 + - TYPE:DELETION IDS:11,1 STRANDS:+-,1 + chr1 547154 547462 chr1 547265 547569 1 0.00254453 + - TYPE:DELETION IDS:10,6 STRANDS:+-,6 MAX:chr1:547175;chr1:547569 95:chr1:547169-547225;chr1:547266-547569 Test data sets ============== @@ -412,7 +421,7 @@ To run lumpy with just the paired-end data, We will assume the mean=500 and stde :: ../bin/lumpy \ -mw 4 \ - -tt 1e-3 \ + -tt 0.0 \ -pe \ bam_file:sample.discordant.pe.sort.bam,histo_file:sample.pe.histo,mean:500,stdev:50,read_length:150,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1\ > sample.pe.bedpe @@ -424,7 +433,7 @@ We can run lumpy with just the split-read data too: :: ../bin/lumpy \ -mw 4 \ - -tt 1e-3 \ + -tt 0.0 \ -sr \ bam_file:sample.sr.sort.bam,back_distance:20,weight:1,id:1,min_mapping_threshold:1 \ > sample.sr.bedpe @@ -436,7 +445,7 @@ Or, we run lumpy with both the paired-end and split-read data: :: ../bin/lumpy \ -mw 4 \ - -tt 1e-3 \ + -tt 0.0 \ -pe \ bam_file:sample.discordant.pe.sort.bam,histo_file:sample.pe.histo,mean:500,stdev:50,read_length:150,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1\ -sr \ @@ -450,7 +459,7 @@ We can run lumpy with paired-end data from a matched tumor/normal samples :: ../bin/lumpy \ -mw 4 \ - -tt 1e-3 \ + -tt 0.0 \ -pe \ bam_file:tumor.pe.sort.bam,histo_file:tumor.pe.histo,mean:500,stdev:50,read_length:150,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1\ -pe \ @@ -486,7 +495,7 @@ We now rerun lumpy with the exclude (-x) option :: ../bin/lumpy \ -mw 4 \ - -tt 1e-3 \ + -tt 0.0 \ -x exclude.bed \ -pe \ bam_file:sample.pe.sort.bam,histo_file:sample.pe.histo,mean:500,stdev:50,read_length:150,min_non_overlap:150,discordant_z:4,back_distance:20,weight:1,id:1,min_mapping_threshold:1\