From SNPs to sequences

Question

[dr.genetics]

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.

[GenoMax]

Converting vcf to fasta format and others.

[dr.genetics]

Thank you so much. Will check it out.

Answer 1

[Brice Sarver]

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.

[dr.genetics]

Awesome! Will try out. Thank you!