Phasing human samples with Eagle 2.4.1.
I have PAR regions on chromosome 23 right now.
I know I can use PLINK 1.9
split-x to move them to chromosome 25, then submit chromosome 23 to Eagle to basically phase only the non-PAR regions.
From reading Eagle the documentation sec 4.1.1 (https://data.broadinstitute.org/alkesgroup/Eagle/), I get the impression that chromosome 23 is phased without PAR regions and that trying to phase PAR regions can be inaccurate. My question is: In general do people just phase 23 non-PAR regions with Eagle?