Closed davmlaw closed 2 weeks ago
I am downloading 111 here on CCB west machine: /data/annotation/VEP/vep_cache
and vg test - /data/annotation/VEP/vep_cache in screen
--hgvsg
and --hgvsg_use_accession
work properly in VEP 111
We've run VEP110 over variantgrid.com - it will take way too long to process everything again - but could we run VEP110 over just the Structural variants?
Added a vep_version to be able to have different command lines for diff vep versions. Used this to use summary stats for SV pipeline
Need to check this is now populated in VG test
http://test.variantgrid.com/variantopedia/view_variant/11500955
Doesn't have any conservation scores in VariantAnnotation (looked in DB)
Needs to show them too again - I think it's hidden for SVs
So, the new ColumnVEPFields were still for Standard/Short only - will need to update them in a migration
Also need to implement a has_conservation or similar to display variant details page
I'm re-running SV pipelines in vg test, this is the only 112 environment so only one affected
Verified conservation now calculation for SV in VEP 112, and appear on variant details page
https://asia.ensembl.org/info/docs/tools/vep/script/vep_download.html#new
We could use summary stats to be able to retrieve conservation scores for SVs
Moved plugins into other issue