Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?