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broadinstitute / tgg_methods

Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
MIT License
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Implement changes to GVS-VETS into Seqr Loading Pipeline #83

Closed matren395 closed 2 months ago

matren395 commented 5 months ago

Variant QC annotations are now stored in the 'FT' field in entries, instead of the 'filters' field. This is now how WARP formatted them. As such, adding VETS Variant QC filters to the appropriate 'filters' field for Seqr needs to be implemented. Since VETS is allele-specific, we may check the VETS 'Score' for each allele and apply filter flags according to their documented threshold (must be below 0.997 for SNPs, 0.99 for Indels)

matren395 commented 2 months ago

This was implemented by myself and Ben B. , reading the 'Callibration_Sensitivy' scores and updating the 'FILTER' field as appropriate