VCF File: remove certain chromosomes

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

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updated 9.1 years ago by Pierre Lindenbaum

• written 9.1 years ago by fire_water

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!

• 0 views • link

written 9.1 years ago by GenoMax

1 answer

or just

grep -Ev '^(GL|NC)' input.vcf

• 0 views • link

written 9.1 years ago by Pierre Lindenbaum

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