Opened 5 months ago

Closed 4 months ago

#1222 closed enhancement (fixed)

Remove the G5 distance calculations from the variant calling script

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.25
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The calculations depend on the G5 flag that existed in dbSNP 151, but it seems like it has been removed in dbSNP 153. The G5 flag is also used in the filter expression. So it needs to be removed from there also, but we believe that the COMMON flag should be enough.

Change History (3)

comment:1 Changed 5 months ago by Nicklas Nordborg

In 5810:

References #1222: Remove the G5 distance calculations from the variant calling script

Removed scripts and files used by the G5 distance calculations.

comment:2 Changed 5 months ago by Nicklas Nordborg

In 5811:

References #1222: Remove the G5 distance calculations from the variant calling script

Removed code for doing G5 distance calculcations and annotations

comment:3 Changed 4 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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