Generating kmers from VCF file

[drtamermansour]

The idea here is to transform each variant to a sequence from the user-defined x nucleotides before the variant to the user-defined z nucleotides after the variant. The user may ask for the reference or the mutant sequence

I am not aware of tool which can do this but there are tools which generate consensus sequence like bcftools consensus which has a way to generate a consensus sequence from a target region of the reference. vcf-consensus has similar behavior