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broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
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Incorrect mCNV genotype counts in MainVcfQc #690

Open mwalker174 opened 3 weeks ago

mwalker174 commented 3 weeks ago

The block of code found here:

https://github.com/broadinstitute/gatk-sv/blob/18efe4b1864945ac81e2b4d08d21652dcd1a63b9/src/sv-pipeline/scripts/vcf_qc/collectQC.vcf_wide.sh#L180

counts hom-alt as CN=0 but should also count CN>=4.