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rwdavies / STITCH

STITCH - Sequencing To Imputation Through Constructing Haplotypes
http://www.nature.com/ng/journal/v48/n8/abs/ng.3594.html
GNU General Public License v3.0
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Impute sex chromosomes properly #46

Open rwdavies opened 3 years ago

rwdavies commented 3 years ago

per-request

GuyReeves commented 2 years ago

is there any advise on imputing sex chromosomes . So far I have only done autosomes, is there are way to do Sex chromosomes.

I believe I have the sex of most or all individuals.

my data is XY Male XX female Drosophila

rwdavies commented 2 years ago

Apologies I never got around to writing this. The simplest thing to do is just run all the samples as if it weren't a sex chromosome. This will be fine for XX samples. For XY samples, imputing the X, it will be slightly less accurate, as all recombinations need to be double recombinations, but it should still work. The right thing to do would be to take sex as an argument and allow the XY samples to have only single recombinations, but alas, that's a future goal