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I would like to extract all the mutations in a single gene of interest from the VCF file. For example I would like to extract all the mutations in the NFKB1 gene from the whole genome VCF file.

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    $\begingroup$ What have you tried? bcftools view has an option to extract by coordinates or by annotation if your VCF had the gene annotation. If you used custom annotation tools, they may have their own filtering utilities. $\endgroup$
    – Ram RS
    Commented Mar 6 at 22:24
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Mar 6 at 23:52

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Find the location of the gene of interest and then filter the vcf for that location using vcftools, bcftools, plink, or some other software. There is a lot of good documentation available online for these tools.

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As mentioned, there are many options to go (eg. vcftools and bcftools). The Broad Institute provides a valuable toolset (GATK) for this very purpose and extended procedures for various variant selection tasks.

SelectVariants function can be good for this purpose, though the location of a gene of interest should be addressed: https://gatk.broadinstitute.org/hc/en-us/articles/13832694334235-SelectVariants

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