Fix missing non reference seq region in VEP cache - Githubissues

Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

https://www.ensembl.org/vep

Apache License 2.0

456 stars 152 forks source link

Fix missing non reference seq region in VEP cache #1718

Closed nakib103 closed 4 months ago

nakib103 commented 4 months ago

ENSVAR-6377 https://github.com/Ensembl/ensembl-vep/issues/1705

In e110, assembly_exceptions table was truncated which contained the sequence region for patches, haploptypes etc. due to changed mechanism of how those regions are showed in Ensembl genome browser.

The VEP cache pipeline depended on the assembly_exceptions table to grab those region. This PR aims to fix these issue by updating the current correct way to add non reference sequence regions.

Test

pipeline url - http://guihive.ebi.ac.uk:8080/versions/96/?driver=mysql&username=ensadmin&host=mysql-ens-var-prod-4&port=4694&dbname=snhossain_dump_vep_human_113_test&passwd=xxxxx