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broadinstitute / GATK-gCNV-publication

Supporting code and materials for GATK gCNV publication
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Create a blacklist for filtering out PAR regions #3

Open asmirnov239 opened 4 years ago

asmirnov239 commented 4 years ago

This is needed for improving sex genotyping performance

samuelklee commented 4 years ago

@JMF47 is this done? If so, can we put the blacklist in the appropriate bucket and document here?

Do we also need to separate out another FilterIntervals step for ploidy determination in the official WDL? I think this is done in the SV WGS WDLs, so perhaps merging those changes will close this issue.