Question: vcftools for a zip file
0
gravatar for xinhui.wang
5.3 years ago by
xinhui.wang220
Netherlands
xinhui.wang220 wrote:

I am running vcftool on multi vcf documents. I could run vcftools with one vcf document and how could I run with a list of vcf documents?

actually. I would like to generate a ped file with many vcf input file. I tried

ls *vcf | xargs vcf-merge > merged.vcf

however, it could not work with an error message as

exited with status 255; abortingxargs: vcf-merge
software error • 1.7k views
ADD COMMENTlink modified 5.3 years ago by RamRS27k • written 5.3 years ago by xinhui.wang220
0
gravatar for RamRS
5.3 years ago by
RamRS27k
Houston, TX
RamRS27k wrote:

Use Linux for loops: http://www.thegeekstuff.com/2011/07/bash-for-loop-examples/

Update: So you're using vcf-merge. I don't see why your title has zip files in it. I also think vcf-merge *.vcf should work thanks to shell globbing.

ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by RamRS27k

In bioinfo data processing, xargs is often safer and more convenient than for loops.

ADD REPLYlink written 5.3 years ago by lh332k

I agree. The for loop suggestion was before OP added details.

ADD REPLYlink written 5.3 years ago by RamRS27k
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