How to filter mutect2 VCF output?

Question

[Whoknows]

Hi

I have ran mutect2 on a Blood and FFPE samples for finding somatic variations; Mutect2 found ~20k mutations,

Actually, I'm new in cancer area and I wonder if anybody help me to find a way to reduce number of mutations.

1- Which field you suggest for filtration?

2- Can I use tool like Vcffilter for this part?

cheers.

Answer 1

[poisonAlien]

Straight forward way to filter mutect2 vcf is to use all variants with PASS filter. Unlike mutect1 which had KEEP or REJECT tags, mutect2 annotates variants with various filters (possible reason why a particular variant is filtered).

Using vcftools something like this

vcftools --vcf foo.vcf --remove-filtered-all --recode --out foo_pass