Question: (Closed) VCF File: remove certain chromosomes
0
gravatar for fire_water
11 months ago by
fire_water70
United States
fire_water70 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 • 470 views
ADD COMMENTlink modified 11 months ago by Pierre Lindenbaum107k • written 11 months ago by fire_water70

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 11 months ago • written 11 months ago by genomax47k
2
gravatar for Pierre Lindenbaum
11 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum107k wrote:

or just

grep -Ev '^(GL|NC)' input.vcf
ADD COMMENTlink written 11 months ago by Pierre Lindenbaum107k
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