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.
MuTect with hg38(GRCh38) reference
I am trying to use Mutect with hg38 as reference to call somatic vatiants for Cancer and Normal data.
I could not find the required hg38 Cosmic vcf file in the help secteion for Mutect (http://www.broadinstitute.org/cancer/cga/mutect_run). The dbsnp vcf I am using is dbsnp_144.hg38.vcf from the hg38 bundle.
How can generate the cosmic vcf file for the hg38 bundle? Any help is appreciated.