Changes between Initial Version and Version 1 of Ticket #1225


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Timestamp:
Jan 28, 2020, 8:29:21 AM (3 years ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1225 – Description

    initial v1  
    11The 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
     2
     3== Summary of changes ==
     4
     5**dbSNP updated to version 153**\\
     6It 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.
     7
     8**COSMIC updated to version 90**\\
     9They 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.