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Port Seqr-Sample-QC into v03_pipeline #544

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bpblanken opened this issue Jul 25, 2023 · 1 comment
Open

Port Seqr-Sample-QC into v03_pipeline #544

bpblanken opened this issue Jul 25, 2023 · 1 comment

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

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