Question: (Closed) VCF File: remove certain chromosomes
0
gravatar for fire_water
9 weeks 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 • 111 views
ADD COMMENTlink modified 9 weeks ago by Pierre Lindenbaum96k • written 9 weeks 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 9 weeks ago • written 9 weeks ago by genomax32k
1
gravatar for Pierre Lindenbaum
9 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum96k wrote:

or just

grep -Ev '^(GL|NC)' input.vcf
ADD COMMENTlink written 9 weeks ago by Pierre Lindenbaum96k
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