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Incorrect mCNV genotype counts in MainVcfQc #690

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mwalker174 opened this issue Jun 12, 2024 · 0 comments · May be fixed by #708
Open

Incorrect mCNV genotype counts in MainVcfQc #690

mwalker174 opened this issue Jun 12, 2024 · 0 comments · May be fixed by #708
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@kjaisingh
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The block of code found here:

gatk-sv/src/sv-pipeline/scripts/vcf_qc/collectQC.vcf_wide.sh

Line 180 in 18efe4b

#Get genotype counts per variant for multi-alleleic CNVs

counts hom-alt as CN=0 but should also count CN>=4.
@mwalker174 mwalker174 added the bug Something isn't working label Jun 12, 2024
@kjaisingh kjaisingh self-assigned this Aug 9, 2024
@kjaisingh kjaisingh linked a pull request Aug 9, 2024 that will close this issue
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@kjaisingh kjaisingh linked a pull request Aug 9, 2024 that will close this issue
Resolve incorrect mCNV genotype counts for hom-alt #708
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Resolve incorrect mCNV genotype counts for hom-alt broadinstitute/gatk-sv
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@mwalker174 @kjaisingh