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gtool conversion error

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 MAP.map \
--phenotype phenotype --sex sex \
--num_snps 498 \
--num_samples 966 \
--chr 11 \
--snp \
--log SORL1.log
gtool snp impute
• 3,408 views • link
updated by Ram Ram • written by jkatz77 • jkatz77

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

gtool -G --g example/example.gen --s example/example.sample
• 0 views • link
updated by Ram Ram • written by zx8754 zx8754

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...

• 0 views • link
updated by Ram Ram • written by jkatz77 • jkatz77

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.

Cheers!

• 1 views • link
updated by Ram Ram • written by zx8754 zx8754

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