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dmiller903 / trioPhaser

An application to phase a trio when gVCF's are available
MIT License
8 stars 1 forks source link

Phasing X-chromosome variants #2

Open karoliinas opened 2 years ago

karoliinas commented 2 years ago

Hi, I ran triophase on a number of families, a really nice tool to take in the trio information as it's not so clear with shapeit4. It left me wondering, though, is there a reason why the X-chromosome isn't included in the analysis? I mean for the girls in the cohort. Thanks!

dmiller903 commented 2 years ago

Hello,

Thank you for using trioPhaser! When I originally created trioPhaser I was doing research on rare diseases that would likely be inherited in a recessive manner through autosomal chromosomes. Therefore, I didn't code in the logic to take X chromosomes into consideration as X-linked, inherited, disease patterns were not on my radar.

karoliinas commented 2 years ago

Ok, thanks!