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ga4gh
Adam English edited this page Aug 2, 2024
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The ga4gh command will consolidate tp-base/fn and tp-comp/fp VCF files into a single truth and query vcf, respectively. Additional tags are added that are compliant with the ga4gh intermediates.
When consolidating a result which has truvari refine, the truvari ga4gh --with-refine flag will extract original variants from unharmonized regions and altered variants from harmonized regions inside the phab_bench/ sub-directory.