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GATK4: Trouble running "GATK 4 CNV Proportional Coverage for Capture"

Sahar90Sahar90 Broad InstituteMember, Broadie


I am trying to run "GATK 4 CNV Proportional Coverage for Capture" on
samples with no matched normals sequenced using TSCA (TrueSeq Custom

I understand that the first step is to run "GATK 4 CNV Proportional
Coverage for Capture" and configure the task replacing
gatk4cnv_padded_target_bed_capture with the bed file with the intervals

I am getting the attached error and stdout. It seems that it doesn't like
the fact that some intervals are overlapping. What is the workaround to

I am running GATK4 workflow because I would like to run absolute to
estimate the purity of the samples. If there is a simpler way to get the
purity of such samples, please let me know.



Best Answer


  • Sahar90Sahar90 Broad InstituteMember, Broadie

    Or, is there a tool that given a .bed file would return another .bed file but with overlapping intervals merged which I could then use in "GATK 4 CNV Proportional Coverage for Capture"?
    Also, what are the main differences between "DepthofCov" task and "GATK 4 CNV Proportional Coverage for Capture". Can the output of DepthofCov be used instead?

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