Unfortunately, this function only supports chromosome numbers 1-23. I work in non-model systems, and have a draft genome with several thousand scaffolds. This is not a problem in plink with the --allow-extra-chr option, but EIGENSOFT doesn't have a way around this to convert those .PED and .MAP files to the .GENO file that I need.
Conversion tools for GWAS
Good morning, actually I'm working for a GWAS for the metabolic syndrome, I've .bed .bim and .fam files also .ped and .map, I'm looking for a tool that allow me to obtain .geno file , because I need to do some research with EIGENSOFT and it needs some file that I can't have right now. There is some tool that is capable to convert some of my file into .geno file.
I need also .ind and .snp and .pca files how can i obtain these files also?
(I apologize for my English I'm not British or American)
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danielestrife •
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You can still work with the PLINK binary files:
cp study.bim study.pedsnp ## Renaming so that Eigensoft can recognize file type
cp study.fam study.pedind ## Renaming so that Eigensoft can recognize file type
smartpca.perl -i study.bed -a study.pedsnp -b study.pedind -o study.pca -p study.plot -e study.eval -m 0 -l study.log
rm study.pedsnp ## removing temp files
rm study.pedsnp ## removing temp files
The CONVERTF program in EIGENSOFT handles this.
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But i can't understand how it works, can you give me an example of command-line rule?
convertf -p params.txtwhere params.txt looks something like:Thank you for your reply. May I ask how can I convert .bed, .bim and .fam files to packedancestrymap format?
Can I also use converf? If so, how should my parameter file look like?
Many thanks!
@joey I will try when possible and i will tell you , thank you so much
@joey It gives me this error:
Have you checked the PATH?
Nope I didn't put that now I will try it,
Those are the errors, I can't figure it out
You need to update your system or download some libraries.
For example in Ubuntu you can install libatlas package using
which should have the
so.3libraryI'm so sorry and I need a little more help
smartpca:(I'm on Ubuntu 14.04)
So..I fixed the problem at last...
I looked at the Makefile and saw that it was calling gfortran
which wasn't there on my file system...
I change it to
FC = gfortran-4.4and recompiled the porgram usingand it's working fine.
Thank you all, thank you Joey
hi,danielestrife.
I have suffered the same problems with you. I'm glad that you have conquered them, but i don't understand how you solve it at the final process as you descripted in this post. Could you give me some help? Thank you!