Opened 6 months ago

Closed 6 months ago

#1361 closed enhancement (fixed)

Use DNA genotyping in the Genotype QC wizards

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.37
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Now that the genotyping information from the blood DNA samples have been integrated into BASE it would be nice if the genotype information could be used by the Genotype QC wizards.

Change History (10)

comment:1 Changed 6 months ago by Nicklas Nordborg

In 6588:

References #1361: Use DNA genotyping in the Genotype QC wizards

The genotype calls are now used in the first Genotype QC wizard. Some changes may cause the Flagged alignment wizard to stop working.

comment:2 Changed 6 months ago by Nicklas Nordborg

In 6589:

References #1361: Use DNA genotyping in the Genotype QC wizards

The "Flagged alignments" wizard should now be able to use the genotyping information from GenotypeCall items.

comment:3 Changed 6 months ago by Nicklas Nordborg

In 6590:

References #1361: Use DNA genotyping in the Genotype QC wizards

Include information about the BeadChip when comparing against genotype calls.

comment:4 Changed 6 months ago by Nicklas Nordborg

In 6591:

References #1361: Use DNA genotyping in the Genotype QC wizards

Errors during pre-loading are now catched and displayed for the user instead of the progress bar getting stuck somewhere in the middle.

comment:5 Changed 6 months ago by Nicklas Nordborg

In 6592:

References #1361: Use DNA genotyping in the Genotype QC wizards

Display bead chip name instead of barcode.

comment:6 Changed 6 months ago by Nicklas Nordborg

In 6594:

References #1361: Use DNA genotyping in the Genotype QC wizards

Create a local copy of VCF files that are located on remote servers. This will improve performance when used in the future.

comment:7 Changed 6 months ago by Nicklas Nordborg

In 6595:

References #1361: Use DNA genotyping in the Genotype QC wizards

Updated the standalone genotype check wizard.

comment:8 Changed 6 months ago by Nicklas Nordborg

In 6596:

References #1361: Use DNA genotyping in the Genotype QC wizards

Found some stray files that should be removed.

comment:9 Changed 6 months ago by Nicklas Nordborg

In 6598:

References #1361: Use DNA genotyping in the Genotype QC wizards

The local copy should not be compressed.

comment:10 Changed 6 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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