Opened 5 months ago

Closed 4 months ago

#1602 closed task (fixed)

Re-factor the imputation and PRS analysis

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v5.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

See #1601.

The imputation analysis should be re-factored so that it create new child items instead of just attaching files to the OncoArray items.

A new subtype ImputedGenotypes with suffix .i should be defined. Annotations are re-assigned as needed.

The PRS analysis may need some minor changes but it should be enough to just attach the result file and score to the ImputedGenotypes item.

Change History (8)

comment:1 by Nicklas Nordborg, 5 months ago

Summary: Re-factor the imputation and PRS analsysis → Re-factor the imputation and PRS analysis

comment:2 by Nicklas Nordborg, 5 months ago

In 7787:

References #1602: Re-factor the imputation and PRS analysis

Added ImputedGenotypes subtype.

comment:3 by Nicklas Nordborg, 5 months ago

In 7788:

References #1602: Re-factor the imputation and PRS analysis

Updated the imputation pipeline so that it create ImputedGenotypes child items. The script need to be modified so that we get the correct name in the resulting VCF files.

comment:4 by Nicklas Nordborg, 5 months ago

In 7789:

References #1602: Re-factor the imputation and PRS analysis

Updated the PRS calculation.

comment:5 by Nicklas Nordborg, 5 months ago

In 7790:

References #1602: Re-factor the imputation and PRS analysis

Removed things that are no longer needed.

comment:6 by Nicklas Nordborg, 5 months ago

In 7791:

References #1602: Re-factor the imputation and PRS analysis

Added ImputationRefPanel annotation so that we can store the which reference panel that was used for the imputation. The only value so far is Phase3_hg38.

comment:7 by Nicklas Nordborg, 5 months ago

In 7792:

References #1602: Re-factor the imputation and PRS analysis

Added a "Imputed genotypes" section in the case summary.

comment:8 by Nicklas Nordborg, 4 months ago

Resolution: → fixed
Status: new → closed
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