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broadinstitute / seqr-loading-pipelines

hail-based pipelines for annotating variant callsets and exporting them to elasticsearch
MIT License
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Port Seqr-Sample-QC into `v03_pipeline` #544

Open bpblanken opened 11 months ago

bpblanken commented 11 months ago

Placeholder ticket with some notes:

Seqr-Sample-QC
    Sequencing metrics
    if it's exome and external
        Platform Level Computation
            For exome samples
            coverage stats, figure out which platform it came from.
            hail function sample_qc, figure out outliers.
            Import tsv into seqr.
    if it's internal
        grab the platorm field
    population inference
    hail's sample qc
    supposed to be after every callset, but is ~ once a quarter.

https://github.com/broadinstitute/tgg_methods/blob/master/tgg/seqr_scripts/seqr_sample_qc.py

bpblanken commented 3 months ago

@larrybabb @sjahl here is the joint methods/seqr work.