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Phasing information for use in downstream tools

Hi,
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)?
Best Answer
-
Geraldine_VdAuwera Cambridge, MA admin
You should check with the makers of the downstream tools whether the informational content of the phasing fields emitted by Hv and GGVCFS satisfies the input requirements of their tools.
Answers
You should check with the makers of the downstream tools whether the informational content of the phasing fields emitted by Hv and GGVCFS satisfies the input requirements of their tools.