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[bugfix] Fix call rate in sample_qc to divide by the total rows. #5773

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merged 2 commits into from Apr 4, 2019

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commented Apr 4, 2019

Fixes #5561

Also improved the implementation of sample and variant qc.

[bugfix] Fix call rate in sample_qc to divide by the total rows.
Fixes #5561

Also improved the implementation of sample and variant qc.
mt = mt.filter_entries(mt.GQ > 5)
mt = hl.variant_qc(hl.sample_qc(mt))

mt.select_cols(mt.sample_qc.call_rate, foo = mt.sample_qc.n_called / n_rows).cols().show()

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@jigold

jigold Apr 4, 2019

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Delete? Not asserting anything?

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@tpoterba

tpoterba Apr 4, 2019

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oops

**e1.call_stats,
'call_rate': hl.float(e1.n_called) / (e1.n_called + e1.n_not_called + e1.n_filtered),
'n_called': e1.n_called,
'n_not_called': e1.n_not_called,

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@jigold

jigold Apr 4, 2019

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does the order of the fields matter for backwards compatibility?

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@tpoterba

tpoterba Apr 4, 2019

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Really any change in schemas could technically break a pipeline, I suppose. I'm comfortable with this, though.

removed shows

@jigold

jigold approved these changes Apr 4, 2019

@danking danking merged commit f25d982 into hail-is:master Apr 4, 2019

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