Dear team,
I am very excited to be able to use phased genotypes for various genetic analyses. Based on GATK best practices, I have generated a VCF using HC/GenotypeGVCF. I noticed phased genotypes were encoded into FORMAT under a special field PGT.
However, some downstream algorithms I use require the phasing information to be present at the GT field of FORMAT.
I wrote a script to simply move PGT information into the GT field, if available, but I was wondering if this moving is appropriate according to you, or whether I should perform additional steps to actually get a proper phased GT field (e.g. using ReadBackedPhasing)?
Thank you very much for your lights,
Best regards,
r