#1018 closed enhancement (fixed)

Updates to HaplotypeCaller step

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.15
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by nicklas)

#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.

Change History (7)

comment:1 Changed 11 months ago by nicklas

(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%.

comment:2 Changed 11 months ago by nicklas

  • Status changed from new to assigned

comment:3 Changed 10 months ago by nicklas

  • Description modified (diff)

comment:4 Changed 10 months ago by nicklas

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

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

comment:5 Changed 10 months ago by nicklas

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

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

comment:6 Changed 10 months ago by nicklas

(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).

comment:7 Changed 10 months ago by nicklas

  • Resolution set to fixed
  • Status changed from assigned to closed
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