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poruloh / Eagle

Haplotype phasing software
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out of order SNPS #14

Closed flinz closed 5 years ago

flinz commented 6 years ago

Hi there,

I am trying to phase some data from plink files and geta warning that ~100 / 600k SNPS are out of order. It seems like these might correspond to multi-allelic SNPs that I have split into two entries with different alleles, at the same positions. As far as I understand from the documentation, these should be supported.

Any hints on resolving this? Thank you!

poruloh commented 6 years ago

Apologies for the slow response. You are correct; the warning message is incorrectly printed when multi-allelic SNPs are split into entries with the same position. I will fix this bug in the next release; for now, you can safely ignore the warning.