Phasing information for use in downstream tools

simono101simono101 London, UKMember
edited November 2015 in Ask the GATK team

I know that HaplotypeCaller outputs physical phasing information in PG and PGT fields, so as not to confuse physical phasing with pedigree based methods, however if I wanted to use the physical phasing information in downstream tools which rely on the | character in the GT tag and the PS identifier tag, is it sufficient to copy this information from the PG and PGT fields into the GT and PS tags respectively for all samples which were genotyped (I notice that the genotype in PGT and GT may not necessarily agree after you run genotypeGVCFs - it looks like genotypeGVCFs updates the called GT from HaplotypeCaller, but the physical phasing information from is unchanged)?

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