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How to Load Succesfully a VCF File with Process_gvcf Stored Procedure? (Doc ID 2058785.1)

Last updated on MARCH 08, 2017

Applies to:

Oracle Health Sciences Cohort Explorer - Version 3.0.2 and later
Information in this document applies to any platform.
When attempting to load a full genome VCF file, process_gvcf stored procedure never finishes.


The following INSERT command never completes:

INSERT INTO W_EHA_GENE_VARIANT_MAP SELECT * FROM W_EHA_VARIANT_GENE_MAP_STG WHERE VARIANT_WID IN (SELECT VARIANT_WID FROM W_EHA_VARIANT_GENE_MAP_STG MINUS SELECT VARIANT_WID FROM W_EHA_VARIANT_GENE_MAP)

Goal

How to Load Succesfully a VCF File with  Process_gvcf Stored Procedure?

When attempting to load a VCF file, process_gvcf stored procedure never finishes with full genome VCF file.

The following insert command never completes:

INSERT INTO W_EHA_GENE_VARIANT_MAP SELECT * FROM W_EHA_VARIANT_GENE_MAP_STG WHERE VARIANT_WID IN (SELECT VARIANT_WID FROM W_EHA_VARIANT_GENE_MAP_STG MINUS SELECT VARIANT_WID FROM W_EHA_VARIANT_GENE_MAP)

 

Solution

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In this Document
Goal
Solution


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