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SACGF / variantgrid

VariantGrid public repo
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BCFTools +Liftover - test, collect, display reject reasons #1091

Closed davmlaw closed 2 months ago

davmlaw commented 5 months ago

See this issue

New release - testing: https://software.broadinstitute.org/software/score/

If it works, we should store then display the liftover failure reject reasons

davmlaw commented 5 months ago

Will need to install updated version of bcftools +liftover plugin, this should be detected by the deployment_check tool

We read and store the reason now, eg:

{ "message": "BCFTools +liftover rejected variant: UnmappedAnchors" }
davmlaw commented 4 months ago

Deleted old liftover, re-ran, verified it came up with unmapped anchor message

http://test.variantgrid.com/snpdb/liftover/view_liftover_run/58

EmmaTudini commented 4 months ago

@davmlaw Will any of these changes affect Shariant?

davmlaw commented 4 months ago

Shariant currently has BCF tools liftover disabled for the next deploy

When it's enabled, you should probably test it, added to "Shariant - BCFTools liftover testing"