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Question: Exclude Mutations from Mutation List
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gravatar for Haiying.Kong
14 months ago by
Haiying.Kong100
Germany
Haiying.Kong100 wrote:

I have a list of mutations as VCF1.vcf, and another list of mutations as VCF2.vcf.

I need to exclude mutations in VCF1.vcf that are appearing in VCF2,vcf, and save the result as a new vcf file.

What could be the most elegant way of doing this?

ADD COMMENTlink modified 14 months ago by Martin Morgan ♦♦ 22k • written 14 months ago by Haiying.Kong100
0
gravatar for Martin Morgan
14 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

This could be a job for VariantAnnotation::filterVcf(), including the prefilter= argument; see the filterVcf vignette available from the VariantAnnotation landing page https://bioconductor.org/packages/VariantAnnotation, as well as help page. It's difficult to provide additional help without knowing what 'appearing in' means in a computational  sense.

ADD COMMENTlink written 14 months ago by Martin Morgan ♦♦ 22k

Thank you so much. The information you provided is more than enough help  :)

ADD REPLYlink written 14 months ago by Haiying.Kong100
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