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.

Set Criteria for GVCF Blocks to Group by DP

asilverasilver cambridgeMember
edited November 2016 in Ask the GATK team

Hi GATK,

I know that currently GVCF Blocks group non-variant sites for which the genotype quality (GQ) is within a certain range. I was wondering if there is way to set the criteria for GVCF Blocks to also group by coverage depth within a certain range. The use case here is I would like to look at the coverage difference between two adjacent non-variant sites for all subjects in a VCF. I would prefer not to use BP_RESOLUTION as the files would be too large and it would be much more convenient to get the information in a single VCF file rather than having to run the DepthOfCoverage tool on each subject.

Thanks,
Ari

Post edited by asilver on

Best Answer

Answers

Sign In or Register to comment.