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broadinstitute / seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
22 stars 20 forks source link

Add SQUIRLS in silico splice annotations #318

Open anneodonnell opened 2 years ago

anneodonnell commented 2 years ago

Interpretable prioritization of splice variants in diagnostic next-generation sequencing (2021)

PMID: 34289339

Pre-computed files: https://squirls.readthedocs.io/en/latest/setup.html Script for offline scoring: https://squirls.readthedocs.io/en/latest/running.html Pre-compiled software version: https://github.com/TheJacksonLaboratory/Squirls/releases

More info compiled by Ikeoluwa: https://docs.google.com/document/d/1AuNvgkQGxBkwpr6Fma2D3Tai2wMbsBtL5HFGEYH63qQ/edit?usp=sharing

lynnpais commented 5 months ago

Extraordinarily high amount of SE work. Decided not to implement for now.

bpblanken commented 3 months ago

@lynnpais some of the SV work we're doing will make this much easier. We can do this in 1-2 days of work now if we'd like to reconsider.

lynnpais commented 3 months ago

Do it around time of the SV work

lynnpais commented 1 month ago

Blocked on migrating Airflow to Luigi