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Set Criteria for GVCF Blocks to Group by DP

asilverasilver cambridgeMember
edited November 2016 in Ask the GATK team


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.


Post edited by asilver on

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