Duplicate VARIANT rows in W_EHA_VARIANT table

(Doc ID 2081620.1)

Last updated on MARCH 31, 2016

Applies to:

Oracle Healthcare Omics - Version 3.0.2 and later
Information in this document applies to any platform.

Goal

There are a lot of duplicate rows for the same position and replace tags with KNOWN and NOVEL.
For example:

select v1.*, v2.row_wid as NOVEL_VARIANT_WID, v2.precision as NOVEL_PRECISION
from w_eha_variant v1, w_eha_variant v2
where v1.chromosome_wid = v2.chromosome_wid
and v1.start_position = v2.start_position
and v1.replace_tag = v2.replace_tag
and v1.status = 'KNOWN'
and v2.status = 'NOVEL';

First 5 rows:
40735225 24 1388544 1388544 KNOWN T/A - 23 1388544 07-OCT-13 40 1 319268956 PRECISE
40736378 24 1423076 1423076 KNOWN T/A - 23 1423076 07-OCT-13 40 1 319262826 PRECISE
40735532 24 1400874 1400874 KNOWN G/C - 23 1400874 07-OCT-13 40 1 2379527902 PRECISE
40736673 24 1429534 1429534 KNOWN G/C - 23 1429534 07-OCT-13 40 1 65062604 PRECISE
40735775 24 1406589 1406589 KNOWN G/C - 23 1406589 07-OCT-13 40 1 210823481 PRECISE

The only noticeable difference is the "status" and "precision".
Why was "NOVEL" row created when there is already a variant row for the same position with same replace tag?
 

Solution

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