Identify if variants are somatic or germline from VCF file

Question

[Rozita]

Hello,

I'd like to ask if there's a way to identify if the variants in a VCF file that has been shared with me are somatic or germline?

I found the following when I type head filename.vcf and I believe that it suggests that the variants that were called are germline. Is that correct or is the line ##parametersName="Generic - Proton P1 - Germ Line - Low Stringency" a generic line that Torrent Variant Caller generates for all VCF files regardless if somatic or germline variants were called?

##fileformat=VCFv4.1
##fileDate=20211208
##fileUTCtime=2021-12-08T13:06:10
##source="tvc 5.12-11 (35c9114) - Torrent Variant Caller"
##parametersName="Generic - Proton P1 - Germ Line - Low Stringency"
##parametersDetails="TS version: 5.12"
##basecallerVersion="5.12-11/35c9114"
##tmapVersion="5.12.11 (35c9114) (201902181535)"
##reference=/results/referenceLibrary/tmap-f3/hg19/hg19.fasta
##contig=<ID=chr1,length=249250621,assembly=hg19>

Thank you!

[Cyriac Kandoth]

One trick is to look for exact code matches in github. For example, I searched for "Generic - Proton P1 - Germ Line - Low Stringency" and found this list of parameters used by Torrent Variant Caller. The list includes "Generic - Proton P1 - Somatic - Low Stringency" as a different configuration. So, I would assume the VCF you have is for Germline variants only. To confirm, you can look for or calculate variant allele fractions (VAF) for each variant in your VCF and see if they are all around 50% or 100% i.e. for heterozygous and homozygous germline variants respectively.

[Rozita]

Thank you very much, this is pretty much what I suspect as well. I didn't know I could look up the exact code match on GitHub, thank you so much for pointing that out, I appreciate it.