newbieinbioinfo

Question

How to find variants which are not present in second file

0

Entering edit mode

4.5 years ago

shubhamkumbhar420 ▴ 40

Hey guys,

I have two VCF files, Now I want variants from file1 that are NOT present in file2. How can I do this?

newbieinbioinfo

vcf • 1.0k views

ADD COMMENT • link updated 4.5 years ago by Pierre Lindenbaum 166k • written 4.5 years ago by shubhamkumbhar420 ▴ 40

score 0 · Answer 1 · 2021-04-26

0

Entering edit mode

4.5 years ago

Pierre Lindenbaum 166k

bcftools isec   -n~10  f1.vcf.gz f2.vcf.gz

ADD COMMENT • link 4.5 years ago by Pierre Lindenbaum 166k

0

Entering edit mode

Thanks for the help! Is there a way I can get output in vcf file containing all fields like chr position ID ref alt filter and INFO column. The above command only gives chr position ref and alt.

ADD REPLY • link 4.5 years ago by shubhamkumbhar420 ▴ 40

1

Entering edit mode

bcftools query

ADD REPLY • link 4.5 years ago by Pierre Lindenbaum 166k