merge vcf file
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8.3 years ago

well I read in one of the post I could do like this, merge both vcf files

cat 2.vcf 4.vcf > 24.vcf

but when I check at my 24.vcf file I miss some of the chr positions from 4.vcf...

so I asume this code is not valid for vcf files right?

Thanks

vcf • 4.0k views
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Yes, you might try using vcftools merge https://vcftools.github.io/examples.html

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ok thanks..I was just wondering if was possible or not....

I try now merge with vcftools

What would be the opposite of merge?

I mean for example I want take out from 4.vcf all gens in comon with 2.vcf

Thanks!

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thanks genomax!

What would be the opposite of merge?

I mean for example I want take out from 4.vcf all gens in comon with 2.vcf

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Google "vcf intersect". That is the operation you're looking for. bedtools should have it.

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ok! thanks a lot ram!

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