merge vcf file
0
0
Entering edit mode
6.3 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 • 3.2k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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!

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

ok! thanks a lot ram!

ADD REPLY

Login before adding your answer.

Traffic: 1359 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6