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Can Depth of the coverage data from GATK3 corrected using CorrectGCBias

pateln13pateln13 Member
edited November 2018 in Ask the GATK team

Hello,

I have coverage data for a large exome cohort obtained from Depth Of Coverage (GATK 3.6+). We are interested in regions with high GC content and would like to correct sample level GC bias. Unfortunately, the BAM files aren't easily accessible. So curious to know if it is possible at all to run CorrectGCBias on this coverage data ?

Given it's doable, do the input file format follows what described here : https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.3/org_broadinstitute_hellbender_tools_exome_CombineReadCounts.php

Thanks,
Nick

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