Are there publicly available tools that can create flanking sequences for a set of variants + sample names based on a VCF file and a reference genome?
I am looking for such a tool that also takes the flanking variants/genotypes in to account of the specified samples. If there are flanking alternative genotypes for the specified samples the nucleotide at that position in the flank should be changed to a IUPAC.
This seems like a to common thing to write something myself.
Something like vcfprimers in vcflib but then with the additional functionality
- to specify just a few variant by ID or positions
- that flanking variants/genotypes of a specified set of samples can be used to put IUPACS in the flanks (the IUPACS cover the reference allele and the alleles of the specified samples at that location)
- handle flanking indels, by either using them in the flanking sequence or giving a warning for these variants