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merge vcf file

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
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written by cristina_sabiers cristina_sabiers

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!

• 1 views • link
written by cristina_sabiers cristina_sabiers

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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written by cristina_sabiers cristina_sabiers

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

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written by Ram Ram

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