merge vcf file

Question

[cristina_sabiers]

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

[hns]

Yes, you might try using vcftools merge https://vcftools.github.io/examples.html

[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!

[GenoMax]

http://vcftools.sourceforge.net/perl_module.html#vcf-merge
https://samtools.github.io/bcftools/bcftools.html#merge

[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

[Ram]

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

[cristina_sabiers]

ok! thanks a lot ram!