Question: Conversion tools for GWAS
1
gravatar for danielestrife
6.5 years ago by
Italy
danielestrife70 wrote:

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 ile 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)

gwaas wide gwas genome • 7.0k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by danielestrife70

But i can't understand how it works, can you give me an example of command-line rule?

ADD REPLYlink written 6.5 years ago by danielestrife70

convertf -p params.txt where params.txt looks something like:

genotypename: mydata.bed
snpname: mydata.map
indivname: mydata.fam
outputformat: PACKEDANCESTRYMAP
genotypeoutname: converted.geno
snpoutname: converted.snp
indivoutname: converted.ind
familynames: NO
ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by chrchang5237.3k

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!

ADD REPLYlink written 4.8 years ago by zhaomengyao0

@joey I will try when possible and i will tell you , thank you so much

ADD REPLYlink written 6.5 years ago by danielestrife70

@joey It gives me this error:

sh: 1: smartpca: not found
OOPS couldn't open file MDC_OMXEX_zcall_QC_pass.pca.evec for reading at ./smartpca.perl line 65.
ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by danielestrife70

Have you checked the PATH?

ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by Joey410

Nope I didn't put that now I will try it,

ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by danielestrife70
smartpca: error while loading shared libraries: liblapack.so.3: cannot open shared object file: No such file or directory
OOPS couldn't open file MDC_OMXEX_zcall_QC_pass.pca.evec for reading at ./smartpca.perl line 65.

Those are the errors, I can't figure it out

ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by danielestrife70

You need to update your system or download some libraries.

For example in Ubuntu you can install libatlas package using

sudo apt-get install libatlas3-base

which should have the so.3 library

ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by Joey410

I'm so sorry and I need a little more help smartpca:

smartpca: /usr/lib/x86_64-linux-gnu/libgfortran.so.1: version `GFORTRAN_1.4' not found (required by /usr/lib/liblapack.so.3)
smartpca: /usr/lib/x86_64-linux-gnu/libgfortran.so.1: version `GFORTRAN_1.4' not found (required by /usr/lib/libblas.so.3)

(I'm on Ubuntu 14.04)

ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by danielestrife70

So..I fixed the problem at last...

I looked at the Makefile and saw that it was calling gfortran

FC = gfortran

which wasn't there on my file system...

I change it to FC = gfortran-4.4 and recompiled the porgram using

make clobber
make install

and it's working fine.

Thank you all, thank you Joey

ADD REPLYlink modified 10 months ago by RamRS30k • written 6.5 years ago by danielestrife70

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!

ADD REPLYlink written 6.0 years ago by snowy0
5
gravatar for Joey
6.5 years ago by
Joey410
Seattle
Joey410 wrote:

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
ADD COMMENTlink modified 10 months ago by RamRS30k • written 6.5 years ago by Joey410
2
gravatar for chrchang523
6.5 years ago by
chrchang5237.3k
United States
chrchang5237.3k wrote:

The CONVERTF program in EIGENSOFT handles this.

ADD COMMENTlink written 6.5 years ago by chrchang5237.3k

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.

ADD REPLYlink written 5.8 years ago by 265mya0
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