VS-1336 - It's not a site FILTER #8773
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… the VCF header has the filter definition in the FORMAT field. Also minor renaming of ExtractCohort argument.
mcovarr
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src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohort.java
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rsasch
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gbggrant
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* Change extract so that when we filter at the genotype level (with FT) the VCF header has the filter definition in the FORMAT field. * Also minor renaming of ExtractCohort argument. * Point to updated truth.
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* Change extract so that when we filter at the genotype level (with FT) the VCF header has the filter definition in the FORMAT field. * Also minor renaming of ExtractCohort argument. * Point to updated truth.
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Change extract so that when we filter at the genotype level (with FT) the VCF header has the filter definition in the comment/unstructured fields of the VCF Header.
Also minor renaming of ExtractCohort argument.
Passing Integration Test (all chromosomes) here
Passing Integration Test (chr20 and friends) here