Flagged alignments wizard

[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.

The wizard will probably require different approaches for different problems:

• High HET: This is probably the easiest to handle. A re-run from RNA or re-extraction is scheduled. When the result arrive there are two outcomes:
  • HET has dropped: Disable the original alignment and accept the re-run.
  • HET is the same: Accept both.

• Qiacube mixup: Schedule re-extractions for samples that was part of the qiacube. We should expect pairs of HIGH/LOW mismatch. The problem can be solved by disabling alignments from the problematic qiacube and accepting the re-runs. Theoretically, the original alignments can be saved by a (complicated) renaming procedure. The secondary analysis part should be deleted and re-executed (since the original names may be part of file data).

• Libplate rotation: More or less the same actions as for a qiacube mixup, but it may be enough the re-run from RNA.