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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.

GATK depth of coverage -L option

Hi GATK team

I am trying to use GATK depth of coverage program to obtain region wise coverage for my samples. I have whole exome seq data for normal and tumor, but done on different kits. When I run GATK depth of coverage program, which bed file would I use for the -L option? I require coverage for every region because I use this to obtain copy number using the ExomeCNV package in R. I would really appreciate any inputs.

Thank you,


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