I have an MAF file with about a couple million SNVs in it from various samples, and I'd like to verify that the file has the right reference bases. Since I'm not really looking for a 'sequence' it seems like querying Ensembl for each one wouldn't be vey efficient. Is there any straightforward way to just submit a table of chromosomes and positions and get the hg19 reference bases at those loci?
A somewhat related question (as it may be why I'm getting 'wrong reference base' errors for a tool I'm trying to use, motivating this post): when an MAF file has a 'start' and 'end' position for an SNV that differ by 1, which one is the actual position of the SNV? Thanks.