Question: How to convert multiple vcf files to a ped file?
2
gravatar for line1438
3.2 years ago by
line143820
line143820 wrote:

I had 421 vcf files, I want to convert the all vcf files to the ped file (format of plink),

and I want to merge these 421 ped files to a ped file, what is the best should I do?

Thanks a lot!

vcftools plink • 2.6k views
ADD COMMENTlink modified 3.2 years ago by Medhat8.5k • written 3.2 years ago by line143820
3
gravatar for Medhat
3.2 years ago by
Medhat8.5k
Texas
Medhat8.5k wrote:

using plink
in the directory that contains your vcf files run this command "assuming that plink in the path"

for i in *.vcf;  do f="${i%.*}"; plink --vcf $i --maf 0.05 --recode --out $f".ped";done

for merging follow this
http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#mergelist

example:

plink --file fA --merge-list allfiles.txt --make-bed --out mynewdata
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Medhat8.5k
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