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vcftools for a zip file

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
• 3,120 views • link
updated by Ram Ram • written by xinhui.wang xinhui.wang

1 answer

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.

• 0 views • link
written by Ram Ram

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
• 0 views • link
updated by Ram Ram • written by xinhui.wang xinhui.wang

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

• 0 views • link
updated by Ram Ram • written by lh3 lh3

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

• 0 views • link
written by Ram Ram

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