I've got VCF-like files with start, stop, REF and ALT columns. I need to check that the REF position from the variants are the same as the one in the genome, to check if they're from the same built. I also need the surrounding nucleotides of the given position. Also, some of the REF columns are empty and because of this, it is not an appropriate VCF file.
I've got a fasta file which has the genome for chromosome 1, and I was wondering if there's a library available to get a part of the genome in nucleotides, given a start- and stop position. For example, if you've got the genome AACCGGTT, that given a start position of 1 and a stop position of 4 it returns AACC. I could write such a parser myself, but I'd rather use a library which has the edge-cases covered.
I'd rather have something locally than use the API of NCBI, which also makes this possible.