When using Eagle, is the X chromosome typically phased without including pseudoautosomal regions?
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16 months ago
curious ▴ 530

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?

Thank you

eagle phasing • 388 views
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