Comments (4)
That is correct; I decided to use alphabetic rather than A1/A2 order for now since plink 1.x normally doesn't try to preserve A1/A2 order. So yes, you should use a short bash script for now if you want REF/ALT-based names.
(plink 2.0 fixes this.)
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Okay, looking forward to 2.0. Is there a dev repo?
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Not yet, but I'll let you know when that changes.
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Forgot to comment here that the plink 2.0 dev repo is now visible.
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