Attention: Want an end-to-end pipelining solution for GATK Best Practices?
Using Mutect2 to call the same variants in multiple tumor samples
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
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?