Opened 7 months ago

Closed 5 months ago

#1031 closed enhancement (fixed)

Define a genotype QC flag that can be set on alignments that has been verified to match another sample

Reported by: nicklas Owned by: nicklas
Priority: major Milestone: Reggie v4.16
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

For example, we have matched the genotype of several alignments to the genotype of DNA extracted from blood. This gives a very good indication that the sample has not been contaminated or swapped during the processing in the lab. Other alignments have been matched against a secondary sample from the same person. It would be useful to know which those samples are since it could help us to identify problems with samples that don't match as expected.

We could for example create a new annotation for alignments QC_GenoTypeVerified with possible values: DNA, Specimen.

Change History (7)

comment:1 Changed 6 months ago by nicklas

  • Status changed from new to assigned

comment:2 Changed 6 months ago by nicklas

(In [4710]) References #1031: Define a genotype QC flag that can be set on alignments that has been verified to match another sample

Added QC_GenoTypeVerified annotation.

comment:3 Changed 6 months ago by nicklas

(In [4711]) References #1031: Define a genotype QC flag that can be set on alignments that has been verified to match another sample

Added "Lysate" option.

comment:4 Changed 6 months ago by nicklas

(In [4712]) References #1031: Define a genotype QC flag that can be set on alignments that has been verified to match another sample

Added VerifiedMatch enum with three options: DNA, SPECIMEN and LYSATE.

The GenoTypeChecker now checks if two alignments are from different specimen or lysates and sets the verified match for a comparison. It will also check if QC_GenoTypeVerified annotation on the alignments and select the strongest match. For example, if an alignment is already annotated with VerifiedMatch.DNA and we get a good match to another alignment the comparison also get VerifiedMatch.DNA even if the other alignment is from the same RNA.

At the moment this is only visible in the Genotype QC wizard. It is not saved when registering.

comment:5 Changed 6 months ago by nicklas

(In [4713]) References #1031: Define a genotype QC flag that can be set on alignments that has been verified to match another sample

The "Genotype summary" dialog now displays the QC_GENOTYPE_VERIFIED and QC_GENOTYPE_COMMENT annotations.

comment:6 Changed 6 months ago by nicklas

(In [4728]) References #1031: Define a genotype QC flag that can be set on alignments that has been verified to match another sample

Lots of changes to GUI that should make it easier to spot comparisons that are made between different specimen/lysate/rna/etc...

The flag is also saved now when registering the comparisons. There are no manual options to override the automatic detection.

comment:7 Changed 5 months ago by nicklas

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