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 the RNA and stop the auto-confirmation 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.

[Nicklas Nordborg]

(In [4658]) References #1018: Updates to HaplotypeCaller step

Changed the QC_GenoTypeHET to QC_GenoTypeHET_PCT and updated all places that used the old value.

The manual and auto-confirmation wizards have been updated to flag the RNA if the HET percentage is over 65%.

[Nicklas Nordborg]

(In [4672]) References #1018: Updates to HaplotypeCaller step

Updated the SNP list. The new list has 213 entries.

[Nicklas Nordborg]

(In [4675]) References #1018: Updates to HaplotypeCaller step

The auto-confirmation check now stop alignments if the HET percentage is over 65%.

[Nicklas Nordborg]

(In [4676]) References #1018 and #1015.

Adding "reads after mask" and HET percentage to the final job status report. Changed the duplication percentage to only use one decimal (also done in the legacy pipeline).