Unable to Extract Variant into VCF File for a Specific Chromosome Position (Doc ID 1999880.1)

Last updated on MARCH 08, 2017

Applies to:

Oracle Health Sciences Omics Data Bank - Version 3.0.1 and later
Oracle Health Sciences Cohort Explorer - Version 3.0.1 and later
Information in this document applies to any platform.

Symptoms

On Oracle Health Sciences Translational Research Center (TRC) 3.0.1 version,
After loading VCF results to patient context, when using the sequencing search criteria only, a cohort of 28 patients was found.
When attempting to extract the variants into VCF file for the specific chromosome position, 0 variants are being returned.
The following error occurs:

ERROR
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STEPS
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The issue can be reproduced with the following steps:
1. Load VCF results to patient context.
2. Using the sequencing search criteria only:
    Sequence Variants:
    * Genotype Genomic Position is chr1:16948379
    * Variant Genotypes Chormosome is 1
    * Variant Genotypes Position is 16948379
    * variant Genotype Scenario is 5
    * Variant Genotype Variant Wid1 is G/A
    * DNA Reference Version Genotype is ENS.73.GRCH38
    * Variant Genotypes is G/A
    * Variant Genotypes2 is Wildtype-G
    The cohort of 28 patients was found.
3. Under "Cohort Viewer"/"Genomic Data Export", when attempting to perform an export after the following selection:
   - Patients IDs source: active query (28), with the context set to 'Patient';
   - Location: At Genomic Position chr1:16948379
   - File Type to Export: Mutation - VCF
   - Export: Immediately

Cause

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