Question: (Closed) VCF File: remove certain chromosomes
0
gravatar for fire_water
4 months ago by
fire_water50
United States
fire_water50 wrote:

I have a few VCF files which contain chromosomes like GL000207.1 or NC_007605. I want to remove all GL* and NC* chromosomes from the VCF files.

Is VCF-tools capable of doing that or does a better approach exist?

Thanks!

sequencing • 165 views
ADD COMMENTlink modified 4 months ago by Pierre Lindenbaum99k • written 4 months ago by fire_water50

Hello fire_water!

See previous answers: How to extract specific chromosome from vcf file

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax34k
1
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum99k wrote:

or just

grep -Ev '^(GL|NC)' input.vcf
ADD COMMENTlink written 4 months ago by Pierre Lindenbaum99k
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