I recently want to use Mach to imputate some SNPs based on 1000 Genome data. Surprisingly, as I followed instruction to chunk ref genome into 10Mb blocks for easy handling, two blocks are of no SNPs at all, one on Chr1 130M-140M, the other on Chr9 50M-60M. So I went back to their allelic.Info file and found there are really big regions without any SNP data. My questions are
- Is it normal or something wrong with Mach's 1000G phaseI v3 file?
- What's special with these regions? difficult to sequence or too much variations?