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SACGF / variantgrid

VariantGrid public repo
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Summary stats - new in VEP 112 - #971

Closed davmlaw closed 2 weeks ago

davmlaw commented 7 months ago

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

davmlaw commented 5 months 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

davmlaw commented 5 months ago

--hgvsg and --hgvsg_use_accession work properly in VEP 111

davmlaw commented 3 months ago

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?

davmlaw commented 1 month ago

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

davmlaw commented 1 month ago

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

davmlaw commented 4 weeks ago

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

davmlaw commented 4 weeks ago

I'm re-running SV pipelines in vg test, this is the only 112 environment so only one affected

davmlaw commented 4 weeks ago

Verified conservation now calculation for SV in VEP 112, and appear on variant details page