obtain common SNPs

0

Entering edit mode

4.5 years ago

a.hasankhani74 • 0

Hi I have two vcf file from two treatment. how can I obtain common snp from this two vcf file?

RNA-Seq • 760 views

ADD COMMENT • link 4.5 years ago by a.hasankhani74 • 0

0

Entering edit mode

Merge the files and look for positions for which both samples have a variant.

ADD REPLY • link 4.5 years ago by WouterDeCoster 47k

0

Entering edit mode

SNPs in each file was 11350. If I want to look for each position It's time-consuming. I'm looking for the fastest way I can.

ADD REPLY • link 4.5 years ago by a.hasankhani74 • 0

0

Entering edit mode

Yes, of course I don't recommend doing this manually. Merge the files and filter for those positions that for both samples have been called.

ADD REPLY • link 4.5 years ago by WouterDeCoster 47k

0

Entering edit mode

how can I merge them? and how can I filter them for those positions that for both samples have been called? Are you have pipeline for these?

ADD REPLY • link 4.5 years ago by a.hasankhani74 • 0

0

Entering edit mode

Have a look at bedtools intersect.

ADD REPLY • link 4.5 years ago by ATpoint 82k

Login before adding your answer.