Hi,
I would like to convert my oxford files into plink format, but without any missing genotypes, so that I can use it in chromopainter.
I guess I have to modify the --hard-call-threshold from 0.1 to 0?
Or can I modify the plink files containing missing genotypes a posteriori so that they are filled in for the missing genotypes?
Any ideas?
Thanks!
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written
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yorgos.athanasiadis •
You can use --hard-call-threshold random a few times; this will randomize genotypes according to the probabilities in the .gen file. i.e., each run will generate a slightly different fileset, and in your subsequent analysis you'll want to look for results which hold across all the filesets.
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written
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chrchang523
Thank you, Chris.
Out of curiosity, is "--hard-call-threshold 0" a bad idea?
That does the opposite of what you want, i.e. it will cause all uncertain genotypes to be set to missing.
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written
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chrchang523
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