Opened 6 years ago

Closed 6 years ago

#1046 closed task (fixed)

Flagged alignments wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.17
Component: net.sf.basedb.reggie Keywords:

Description (last modified by Nicklas Nordborg)

This is the second step in the genotype QC. Alignments that were flagged by the first wizard should be further examined and it should be possible schedule re-runs from RNA or re-extractions from the specimen.

It was not so easy to write a specification for this wizard. Instead, I will write something about the ongoing development as soon somethings seems reasonably stable to be useful.

A description of the development so far

The wizard will start out in a context-less mode which simply means that it will load all alignments from the Flagged alignments list and compare them to each other. In this mode it will make two simple checks:

  1. Check the QC_GENOTYPE_VERIFIED annotation. This is very useful since it allows us to know alignments that we believe to be correct.
  2. Other alignments that has a HIGH or LOW mismatch against a verified alignment is marked as a Verified mismatch. This is an alignment that we believe to be incorrect.

This will be listed together with information about the QiaCube and LibPlate information. The user may click on a QiaCube or LibPlate. This switches the wizard to a context-sensitive mode.

In the context-sensitive mode the wizard will load all alignments (including non-flagged alaignemts) that are related to the context. For example, for a given QiaCube run, the wizard will load all RNA items and follow them up to the Patient level and loading all alignments related to those patients.

In addition to the two simple checks above, the wizard will now also make a third check that will try to locate a possible mixup in the current context. Here is an outline of the procedure:

  • Look for a pair of alignments A1 and A2 where
    • A1 is in the current context
    • A2 is in another context or a VERIFIED alignment
    • there is a LOW mismatch warning between A1 and A2. This indicates that A1 and A2 is from the same patient.
  • Get the patient from A2 and try to find another alignment A3 in the current context that has the same patient. A3 must not be a "Verified mismatch".
  • If we find it, this could mean that A1 is actually A3.
  • This may not be enough information to identify the problem. Typically, a VERIFIED alignment is needed to be sure.

Change History (7)

comment:1 by Nicklas Nordborg, 6 years ago

Status: newassigned

comment:2 by Nicklas Nordborg, 6 years ago

(In [4781]) References #1046: Flagged alignments wizard

Added link on the start page. Required role is set to PrepCurator (same as for the Flagged RNA wizard).

Counter service update to also return the number of flagged alignments.

comment:3 by Nicklas Nordborg, 6 years ago

Description: modified (diff)

comment:4 by Nicklas Nordborg, 6 years ago

(In [4794]) References #1046: Flagged alignments wizard

The first prototype of the wizard. The focus is on getting the wizard to be usable for identifying potential problems related to a QiaCube run or LibPlate (High HET need further development).

There are not options for resolving problems or schedule re-extraction or re-processing.

comment:5 by Nicklas Nordborg, 6 years ago

(In [4797]) References #1046: Flagged alignments wizard

Several updates to the wizard:

  • Two different sets of colored highlights (use CTRL/ALT/SHIFT + click to access the secondary color)
  • Added links to "Case summary"
  • Filters are display on one line
  • Added a "Recently used filters" list
  • No 'context-specific' analysis in the quick update of the table before additional alignments has been loaded
  • Detect if there is a mismatch between two VERIFIED alignments. It should not happen, but if it does something is incorrectly registered.
  • Messages that lead to a "Verified mismatch" are not trusted, which is indicated with line-through styled text.

comment:6 by Nicklas Nordborg, 6 years ago

(In [4799]) References #1046: Flagged alignments wizard

More minor changes:

  • Mark common/different parts of alignments names
  • Display patient name when suggesting a mixup position to make it clearer that it is actually the patient name that is used to find the other position.

comment:7 by Nicklas Nordborg, 6 years ago

Resolution: fixed
Status: assignedclosed

Closing this ticket now since we believe the wizard to be usable for investigating problems.

Support for scheduling re-extractions and handling final flagging/unflagging will be added later.

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