bcftools error about hap.py

[pkrusche]

I am not sure whether the upper and lowercase issue is the only problem here -- it appears that some of the VCF positions are out of order also. I think perhaps the easiest way to fix this would be to use a reference + VCF files where the character case is consistent.

Another thing to try could be to use hap.py --engine=scmp, which is quite similar to som.py.