Question: Convert from oxford to plink format with no missing genotypes
0
gravatar for yorgos.athanasiadis
5.2 years ago by
Denmark
yorgos.athanasiadis40 wrote:

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!

plink chromopainter impute2 • 2.1k views
ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by yorgos.athanasiadis40
1
gravatar for chrchang523
5.2 years ago by
chrchang5237.1k
United States
chrchang5237.1k wrote:

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.

ADD COMMENTlink written 5.2 years ago by chrchang5237.1k

Thank you, Chris.

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

ADD REPLYlink written 5.2 years ago by yorgos.athanasiadis40

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

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by chrchang5237.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1175 users visited in the last hour