I have problem with ambiguous base in SNPdb (BQSR) file and reference genome. The first 2 line of SNPdb (BQSR) looks like:
CHROM POS ID REF ALT QUAL FILTER INFO 1 162362 rs477108567 G A . . .
so that seems in position 162362 in 1 chromosome in my reference genome I should expect G, but there is A. What is a problem. Those 2 files represent the same reference. Any ideas?
Thank you in advance.