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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.
Query reagrding somatic variant calling
I had a query regarding variant calling.
I have three tissues from the same patient (Tumor, Non-Tumor, and Blood)
I wanted to identify the somatic variants and distinguish them from the germ-line variants.
How should i go about with the comparison?
1) Call the variants in all the 3 tissues separately using Haplotype caller?
2) Call Tumor and Non-Tumor using Mutect2 and Blood using Haplotype caller?
3) Make 3 ways comparison using Mutect2 with each of the tissues?
Any document/post discussing this would also be helpful!!
Thanks a lot in advance