Opened 21 months ago
Closed 21 months ago
#1324 closed task (fixed)
Implement support for indexing VCF files from the targeted genotyping
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
---|---|---|---|
Priority: | major | Milestone: | Variant Search v1.2 |
Component: | net.sf.basedb.varsearch | Keywords: | |
Cc: |
Description
See Reggie ticket #1323. The VCF files should be more or less compatible with the existing once from the regular variant calling. But there are some differences:
- Each VariantCall may have multiple VCF files from targeted genotyping. The should all be indexed in the same index.
- The AF (Allele frequency) and VD (Variant Depth) fields are not added by the HaplotypeCaller, but they can be calculated from the AD and DP fields.
- The VCF files also contain results for homozygous genotypes. They should be indexed since it may be useful to query everything, but some functions and information need to be changed since they are not all variants.
Change History (12)
comment:1 Changed 21 months ago by
comment:12 Changed 21 months ago by
Resolution: | → fixed |
---|---|
Status: | new → closed |
Note: See
TracTickets for help on using
tickets.
In 6371: