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Phasing information for use in downstream tools
I know that HaplotypeCaller outputs physical phasing information in
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
PGT fields into the
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)?