gVCF load slow perfomance and VCF load missing rows in the ODB due to column size too small.

(Doc ID 2237513.1)

Last updated on JULY 11, 2017

Applies to:

Oracle Healthcare Omics - Version 3.1 and later
Information in this document applies to any platform.

Symptoms

  • Bug 25414516: The gVCF loader uses external tables to read the data from a VCF format file. One column used for this is an ID column which was sized to be only 50 characters. When a user file exceeds this size, the entire row of data is not loaded into the database (includes variants and sequencing records).
  • Bug 24558261: The gVCF loader had one intermediate table used that links variants to genes based on location, and this SQL was not using nested loops. The result of this was that the SQL execution was taking upwards of several hours for this one intermediate table.


EXPECTED BEHAVIOR
-----------------------

Expect TRC 3.1.0.3 VCF loader to have all rows in ODB and also gVCF loader to take reasonable time.


STEPS
-----------------------

Bug 25414516:

The issue can be reproduced at will with the following steps:

Cause

Sign In with your My Oracle Support account

Don't have a My Oracle Support account? Click to get started

My Oracle Support provides customers with access to over a
Million Knowledge Articles and hundreds of Community platforms