Convert from oxford to plink format with no missing genotypes

Question

[yorgos.athanasiadis]

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!

Answer 1

[chrchang523]

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.

[yorgos.athanasiadis]

Thank you, Chris.

Out of curiosity, is "--hard-call-threshold 0" a bad idea?

[chrchang523]

That does the opposite of what you want, i.e. it will cause all uncertain genotypes to be set to missing.