Is there some utility that will take as input a reference sequence in fasta format and a file of variant calls, with both SNPs and short indels (i.e. VCF or similar), and output a new sequence, identical to the input reference except with the new variants introduced?
It wouldn't be a super tricky thing to script, but since it seems like something that would be relatively common to want to do, I'm wondering if there isn't already some available tools for doing this. Yet I haven't found any.
For simplicity let's assume a single haploid chromosome (trickier for diploid individuals with heterozygous calls).
reference sequence: AAATTTAGAA variant calls: POS REF ALT 2 A C 5 TT T 8 G GCC 10 A T new sequence: ACATTAGCCAT