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From SNPs to sequences

Suppose you have a list of SNPs in a VCF, and you want to get the sequence within a gene, say, BRCA1, then my question is whether there is a tool that can do that -- taking the VCF with a list of SNPs & the name of a gene as input, get a genomic sequence with the specified SNPs within the specified gene?

Thanks.

assembly snp genome gene
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updated by Brice Sarver Brice Sarver • written by dr.genetics dr.genetics

Thank you so much. Will check it out.

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written by dr.genetics dr.genetics

1 answer

You can use the GATK's FastaAlternateReferenceMaker to place the SNPs back in the context of your reference. You can then rip out the gene using a variety of approaches, like bedtools' getfasta.

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written by Brice Sarver Brice Sarver

Awesome! Will try out. Thank you!

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written by dr.genetics dr.genetics

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