Question: (Closed) gtool conversion error
gravatar for jkatz77
4.6 years ago by
United States
jkatz7730 wrote:

I am trying to convert a .gen file to a .map and a .ped file using gtool. The problem is, despite having 498 SNPs in my Gen file, the map file being created only has the first snp and is only 1 row long. The command I am using is:

gtool -G --g GENE.gen \
--s SAMPLE.sample \
--ped PED.ped \
--map \
--phenotype phenotype --sex sex \
--num_snps 498 \
--num_samples 966 \
--chr 11 \
--snp \
--log SORL1.log
snp impute gtool • 1.9k views
ADD COMMENTlink modified 12 months ago by zx87547.1k • written 4.6 years ago by jkatz7730

It is hard to tell without data, did you try running with default settings?

gtool -G --g example/example.gen --s example/example.sample


ADD REPLYlink written 4.6 years ago by zx87547.1k

Thanks for your help! It got me thinking about the problem at a more basic level, and I realized the real issue is I contaminated my .gen file. The problem is, I want to manipulate the file in excel, but once I save the file as a txt or just as the original gen file it ends up not working properly with gtool...

ADD REPLYlink written 4.6 years ago by jkatz7730

A: Bioinformatic Cartoon

ADD REPLYlink written 4.6 years ago by zx87547.1k

Hello jkatz77!

We believe that this post does not fit the main topic of this site.

Not reproducible, OP had a corrupted input gen file, avoid using Excel.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 12 months ago by zx87547.1k
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