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Published 20 hours ago • verified publisher icon Illumina

How to annotate the somaticSV.vcf file?

Open pandafish123 opened this issue 4 years ago • 2 comments

I successfully detected SV using Manta. When deal with the somaticSV.vcf file using Annovar, i encounter with some error.
command line: perl convert2annovar.pl -format vcf4 -allsample -withfreq somaticSV.vcf > sample.annovar

Error: invalid record in VCF file: the GT specifier is not present in the FORMAT string: <chr1 146494079 MantaBND:31106:0:1:0:0:0:1 T T]chr1:149064670] . MinSomaticScore SVTYPE=BND;MATEID=MantaBND:31106:0:1:0:0:0:0;IMPRECISE;CIPOS=-31,31;SOMATIC;SOMATICSCORE=23;BND_DEPTH=80;MATE_BND_DEPTH=38 PR 18,0 23,5>

pandafish123 avatar Dec 04 '19 07:12 pandafish123

@pandafish123 I caught the same problem. Did you fix it?

wanhui5867 avatar Jun 10 '20 16:06 wanhui5867

@pandafish123 I caught the same problem. Did you fix it?

I use VEP instead.

pandafish123 avatar Jun 11 '20 01:06 pandafish123