Opened 5 years ago
Last modified 5 years ago
#1160 closed task
Investigate changes in Picard since our last modified version — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | critical | Milestone: | Reggie v4.23 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
We are using a modified version of Picard for demuxing. It is base on Picard 1.128 and changes are listed on our BASE-hacks site: http://dev.thep.lu.se/basehacks/wiki/Picard
The MIPs pipeline is using UMI (unique molecular indices) which require that 'M' is used in the READ_STRUCTURE parameter to Picard. This is not supported in our modified version, but works in a later version (for example: 2.20.0).
However, we may not be able to just switch to the newer Picard due to our modifications. This ticket is about investigating potential issues.
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