Ensemble.sSNV.tsv does not have some vardict variant. about somaticseq HOT 8 CLOSED

if_VarDict should be 1, if that variant has PASS and Somatic in the VarDict's vcf file.

from somaticseq.

yes,

the variant info is
chr1 3712588 . G A 103 PASS STATUS=StrongSomatic;SAMPLE=TUMOR;TYPE=SNV;DP=91;VD=12;AF=0.1319;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.07143;SOR=0;LSEQ=AGGCTCTGCAGGCGCGGGGC;RSEQ=CAGCGCGCCAGGTCGGCTGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:91:12:5,7:37,42:79,12:0.1319:2,2:38:1:29:1:0.76749:1.23051:60:11:0.131:0.011:1.7 0/0:21:0:0,0:8,13:21,0:0:2,0:36.4:1:33.6:1:1:0:60:9.5:1:0:0.6

but Ensemble.sSNV.tsv has if_VarDict:0

Jeongmin

from somaticseq.

You can send me some of the two files if you don't mind. Include the line in question, plus 10 lines before and after, and also include the headers. You may send them to [email protected].

from somaticseq.

Hi,

i send you file via e-mail.

i think Vardict's 'bed_intersector' step has that problem.  because intersect.vardict.vcf has no variant chr1 3712588 i wrote on issues.

Thank you for your helping.

Jeongmin

from somaticseq.

I figure out why. When VarDict outputs things like <DUP>, <DEL>, <INV>, etc. in the VCF file, they do not have END=xxx field in INFO, which is required for bedtools because the END field tells bedtools where the region ends. So bedtools doesn't go into completion. Let me modify my codes to get around that issue.

from somaticseq.

I incorporated the fix into the "latest" branch. Will move that into the main branch when I've tested it more extensively.

from somaticseq.

oh, great!
i hope it will work fine.

Thank you for your helping.

Jeongmin

from somaticseq.

Fixed by including a routine to remove incompatible lines in VarDict's vcf files before using bedtools on it.

from somaticseq.