ga4gh - ACEnglish/truvari GitHub Wiki

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.