Are there any tools that can extract somatic variants from matched normal tumor vcf files?

Question

[Sandeep]

Hello all, I have a set of VCF files of normal and tumor samples. Are there any tools available to get the somatic only variants from the vcf files? I have checked the post here but found it inconclusive.

Answer 1

[Kevin Blighe]

Sounds like you have unpaired data and just want to filter for variants that are only called in tumour?

I would merge them all together (bcftools merge), or just merge them into their respective tumour and normal groupings; so, you would have 2 final VCFs: tumour.vcf and normal.vcf. I would then create a unique key that identifiers each variant found in each group (CHR:POS:REF:ALT), and then cross-compare with a simple script like awk. You could also set the ID field to be this unique key.

Another way is to merge all files together and then use SnpSift CaseControl, but only checking the allele tallies at the end.

Kevin