Support gnomAD SVs in custom variant lists

broadinstitute / genetic-prevalence-estimator

https://genie.broadinstitute.org/

BSD 3-Clause "New" or "Revised" License

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Support gnomAD SVs in custom variant lists #98

Closed nawatts closed 3 months ago

sambaxter commented 7 months ago

Reminder that these can only be added manually through a custom list or add variant to recommended list.

Sam will ask Heidi about merging columns but for now gnomAD ID will stay the same VEP consequence in genie will be consequence and class stitched together Position and size will go into HGVSc

sambaxter commented 6 months ago

After talking to Heidi this is the model for merging the SV and SNV:

gnomAD ID will both go in same column
Consequence and class stitched together will go into VEP consequence, rename column to "Consequence"
Convert SVs into HGVS g.Chr_Pos_Pos Del (or what else the consequence is) and put it into HGVSc
Use HGVSp for Size and put some sort of disclaimer as a hover hover for SVs the explains "HGVSp is repurposed for SV size"
Put NC# in where transcript is (if it is available in hail table)