Opened 5 years ago
Last modified 5 years ago
#1225 closed enhancement
Update databases used in variant calling pipeline — at Version 1
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | blocker | Milestone: | Reggie v4.25 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description (last modified by )
The aim is to update all databases that has been updated since the original variant calling pipeline. Most of the work is done outside of Reggie. Some changes and information can be found here http://onk-wiki.bmc.lu.se/trac/scanbprim/browser/scanbprim/support-files/variant-calling
Summary of changes
dbSNP updated to version 153
It contains a lot more variants than before. Some of the fields have been removed. We no longer annotate with CDA, G5 or G5A. See also #1222.
COSMIC updated to version 90
They have made major changes to ID assignment and how samples are reported. This affected the custom scripts for calculating mutation frequencies. This was solved by matching ID+GENE from the VCF to ID+GENE in the sample mutation table. The end result should be compatible with older version of COSMIC.
