Updates to HaplotypeCaller step

[Nicklas Nordborg]

#1001 introduced the HaplotypeCaller step for genotyping. We should make some improvements to it:

• A longer list with SNP:s to check (~200+) should give us better sensitivity for contamination (HET > 65%).
• Instead of storing the HET count we should store the HET%
• The auto-confirmation step should flag (but not stop) the RNA if the HET% is high. This will allow an admin to use the "Flagged RNA" wizard to re-schedule a new library prep from the RNA for a second try.