Opened 2 weeks ago

Closed 2 weeks ago

#1589 closed enhancement (fixed)

Add support for haploid genotypes

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Variant Search v1.11
Component: net.sf.basedb.varsearch Keywords:
Cc:

Description

We are updating the genotypes from the OncoArray dataset so that regions in chrX and chrY that are hoploid (depending on gender) are coded as 0, 1 or . instead of 0/0, 1/1 and ./.

The current indexing and search functionality will probably have some problems with them.

Change History (4)

comment:1 by Nicklas Nordborg, 2 weeks ago

In 7684:

References #1589: Add support for haploid genotypes

The OncoArray index should now work (by converting the genotypes to diploid variants).

comment:2 by Nicklas Nordborg, 2 weeks ago

In 7685:

References #1589: Add support for haploid genotypes

Searching should now work also for the imputed index.

comment:3 by Nicklas Nordborg, 2 weeks ago

In 7686:

References #1589: Add support for haploid genotypes

Regular indexing should now also work for haploid genotypes. Note that the genotype will be converted to a diploid in the index but the actual value that is stored is the haploid value.

comment:4 by Nicklas Nordborg, 2 weeks ago

Resolution: → fixed
Status: new → closed
Note: See TracTickets for help on using tickets.