vcf of SV (structural variant): how to retrieve/separate Germline and Somatic SVs?
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.
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