Question: Removing common SNPs from a set of VCF files
0
gravatar for Lina F
2.6 years ago by
Lina F160
Boston, MA
Lina F160 wrote:

Hi all,

I am looking to generate a list of SNPs that are unique to different samples.

To that end, I used bcftools to generate a list of common SNPs for each sample as follows:

# for 9 samples
bcftools isec -p intersection -n =9 *vcf.gz

Now I am trying to subtract the common SNPs from the original VCF files to get the SNPs that are unique to each sample. I assume this should also be possible using bcftools but I could not find a "subtract" command.

Any advice is appreciated!

filtering snp vcf • 1.9k views
ADD COMMENTlink written 2.6 years ago by Lina F160
4
gravatar for ATpoint
2.6 years ago by
ATpoint35k
Germany
ATpoint35k wrote:

Have a look at the --complement option within isec. It prints all entries but the ones that you supply in B.

ADD COMMENTlink written 2.6 years ago by ATpoint35k

Great, thanks for pointing me in the right direction!

ADD REPLYlink written 2.6 years ago by Lina F160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 854 users visited in the last hour