Using Mutect2 to call the same variants in multiple tumor samples

FPBarthelFPBarthel HoustonMember
edited August 2018 in Ask the GATK team

Hi,

I want to use M2 to call variants in multiple tumor samples (from the same individual) and have followed the great guide by @shlee here. Let's assume I have one normal control N and three tumor samples T1, T2 and T3. After calling and filtering variants I am left with three VCF files, eg.

T1-N.filtered.vcf
T2-N.filtered.vcf
T3-N.filtered.vcf

I want to merge these three VCF files so that each variant is genotyped in each tumor sample and the normal sample. The resulting merged VCF file should have a header like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  N    T1    T2    T3

Is there a recommended workflow for this?

Thanks!
Floris

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