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Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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How to annotate the somaticSV.vcf file? #206

Open pandafish123 opened 4 years ago

pandafish123 commented 4 years ago

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>

wanhui5867 commented 4 years ago

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

pandafish123 commented 4 years ago

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

I use VEP instead.