Hello, I encountered error while dealing AnnotSV with vcf file output from Delly.

[minn333]

AnnotSV version: AnnotSV_3.0.9

Command line:
$ANNOTSV/bin/AnnotSV -SVinputFile $files -genomeBuild GRCh37 -outputFile "${files%%.}"_output_t3.tsv -svtBEDcol 4 >& "${files%%.}"_out.log

The error.log as below:

AnnotSV
130109_AnnotSV_inputSVfile.formatted.sorted.bed -b path to/AnnotSV/Annotations_Human/Genes/GRCh37/genes.RefSeq.sorted.bed -wa -wb > path to/$SampleID_delly_sv_output_t3.tsv.tmp.tmp
Error: Invalid record in file path to/20220505-130109_AnnotSV_inputSVfile.formatted.sorted.bed. Record is
17 -54 1077 BND $SampleID BND00215903 A ]chr14:33953985]A 180 LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.7;END=512;CHR2=chr14;POS2=33953985;PE=3;MAPQ=60;CT=5to3;CIPOS=-565,565;CIEND=-565,565 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-15.2495,0,-249.25:152:PASS:23011:46179:23168:2:44:5:0:0
Exit with error

Delly VCF file (extraction error line)
chr17 511 BND00215903 A ]chr14:33953985]A 180 LowQual IMPRECISE;SVTYPE=BND;SVMETHOD=EMBL.DELLYv0.8.7;END=512;CHR2=chr14;POS2=33953985;PE=3;MAPQ=60;CT=5to3;CIPOS=-565,565;CIEND=-565,565 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-15.2495,0,-249.25:152:PASS:23011:46179:23168:2:44:5:0:0

attached vcf file as xlsx file for test as below:

sampleIDforGithub_delly_sv.vcf.xlsx

[lgmgeo]

Hi @minn333,

This is an annotation bug (with AnnotSV) rather than a visualization bug (with knotAnnotSV).

Your confidence interval around the start position is CIPOS=-565,565.
AnnotSV evaluates this start position as follows: start = 511 - 565 = -54
Of course, this negative coordinate is not possible... and causes the bug.

Please, use AnnotSV with the -includeCI option set to "no", this should solve your bug.

I will add a bugfix for that in the future python version.

Best regards,
Véronique

[minn333]

Hello @lgmgeo
Thanks for your kindly reply and solving my problem, I will try as your suggestion.

[minn333]

Dear @lgmgeo
I ran the AnnotSV as your suggestion, the tools didn't go smoothly to the output files. The files I got is listed as below:
$SampleID.SV_RE_intersect.tmp
$SampleID_output.tmp
$SampleID.unannotated.tsv
and log file.

The content of log file as below. Could you kindly tell me what the problem I had met?

Thanks,...
by Duan

 ******************************************
    AnnotSV has been run with these arguments:
    ******************************************
    -REreport no
    -SVinputFile $path/$SampleID_delly_sv.vcf
    -SVinputInfo 1
    -SVminSize 50
    -annotationMode both
    -annotationsDir $Path/AnnotSV/AnnotSV_v3.0.9/share/AnnotSV
    -bcftools bcftools
    -bedtools bedtools
    -candidateGenesFiltering no
    -genomeBuild GRCh37
    -includeCI no
    -metrics us
    -minTotalNumber 500
    -organism Human
    -outputDir $Path-to-output directory
    -outputFile $SampleID_delly_sv_output_t3.tsv
    -overlap 100
    -overwrite yes
    -promoterSize 500
    -rankFiltering 1 2 3 4 5 NA
    -reciprocal no
    -samplesidBEDcol -1
    -snvIndelPASS 0
    -svtBEDcol 4
    -tx RefSeq
    ******************************************

max length of a Tcl list (536870909 elements) exceeded
while executing
"lappend L_allRegulatedGenes {*}[split [lindex $Ls end] ";"]"
(procedure "regulatoryElementsAnnotation" line 45)
invoked from within
"regulatoryElementsAnnotation $L_allGenesOverlapped"
(procedure "genesAnnotation" line 386)
invoked from within
"genesAnnotation"
(file "$path/AnnotSV/AnnotSV_v3.0.9/bin/AnnotSV" line 270)

[lgmgeo]

I think you are trying to annotate a very large SV input file.

Please refer to this:
lgmgeo/AnnotSV#15 (comment)

The future reimplementation in Python should fix this bug.
Sorry for the inconvenience.

[minn333]

Dear @lgmgeo
Thanks for your kindly reply. I had met another problem while running smaller VCF files. The log file as below:
the problem of overlap -100?, how can i solve this problem to finish my annotation?

Thanks..

---

...checking the annotation data sources

WARNING: No GeneHancer annotations available.
(Please, see in the README file how to add these annotations. Users need to contact the GeneCards team.)

...listing arguments
******************************************
AnnotSV has been run with these arguments:
******************************************
-REreport no
-SVinputFile /$path/Delly_smallfiles/$sampleID_delly_sv.vcf
-SVinputInfo 1
-SVminSize 50
-annotationMode both
-annotationsDir /$path/AnnotSV/AnnotSV_v3.0.9/share/AnnotSV
-bcftools bcftools
-bedtools bedtools
-candidateGenesFiltering no
-genomeBuild GRCh37
-includeCI no
-metrics us
-minTotalNumber 500
-organism Human
-outputDir /path/Delly_smallfiles
-outputFile $sampleID_delly_sv_output_t3.tsv
-overlap 100
-overwrite yes
-promoterSize 500
-rankFiltering 1 2 3 4 5 NA
-reciprocal no
-samplesidBEDcol -1
-snvIndelPASS 0
-svtBEDcol 4
-tx RefSeq
******************************************

...searching for SV overlaps with a gene or a regulatory elements
...28035 genes overlapped with an SV

[lgmgeo]

Hi @minn333,

Can you please post your issue in AnnotSV?
It is not the rigth place here (you're in the knotAnnotSV github).

Regarding on your description, I can't see any error message.
Can you give me all the AnnotSV output ? (in a new issue)

Best,
Véronique

[lgmgeo]

cf lgmgeo/AnnotSV#125 (comment)

Thomas, can you close this issue?