Tools to filter Mutect2 output
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5.7 years ago
nanana ▴ 110

I've followed the GATK best practices for tumour normal somatic mutation calling with Mutect2:

1. Run Mutect2 using --artifact_detection_mode on each normal sample from the same sequencing run.
2. Combine all calls made in the above step into a panel of normals (PON) using CombineVariants
3. Run Mutect2 on each tumour normal pair + PON to make somatic calls

I'm then decomposing complex SNPs into single SNPs using vt decompose_blocksub | vt normalize and selecting the SNPs using SelectVariants --excludeFiltered -selectType SNP

I now have vcf files with somatic SNPs called by Mutect2, and I'm looking to do some custom filtering. I have used tools in the past such as vcftools and vcffilter to filter single-sample vcfs. However, vcffilter doesn't seem to work so well with multi-sample (i.e. tumour normal) vcfs - the vcf produced by Mutect2 puts the normal sample in the fist sample column, so using vcffilter -f "AF > 0.075" for example filters the AF of the normal sample.

Are there any recommended tools that I can use to filter Mutect2 vcf output, rather than re-inventing the wheel (again)?

genome SNP • 3.6k views
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It would be good to know what exactly your filtering criteria are. Is it some simple text-based filtering or more complex tasks such as annotating against a database and removal in case of a match?