vcf of SV (structural variant): how to retrieve/separate Germline and Somatic SVs?
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18 months ago
Emily072020 ▴ 10

I have two samples: control and tumor.

After comparing to reference genome, I got a vcf file (for SVs) as shown below:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT   control tumor
chr1 10023 DEL00000011     C       <DEL>   .       PASS    IMPRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLY;CHR2=chr1;END=10123;PE=6;MAPQ=20;CT=3to5;CIPOS=-104,104;CIEND=-104,104  GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV   0/0:0,-12.7796,-242.22:128:PASS:498:1024:485:1:63:3:0:0 0/0:0,-16.9201,-408.134:10333:PASS:588:1179:427:1:78:3:0:0

In this vcf, the germline and somatic SVs are all included. I want to, based on column 9 to 11, retrieve germline SVs and somatic SVs separately. Is there already a pipeline existing for this purpose? Thanks.

vcf sequencing genome Structural variant • 521 views
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