Support unknowns in pedigree #795
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| @@ -202,7 +202,6 @@ def test_get_families_failed_sex_check(self): | |||
| [ | |||
| [ | |||
| 'Sample ROS_006_18Y03226_D1 has pedigree sex F but imputed sex M', | |||
| 'Sample ROS_006_18Y03227_D1 has pedigree sex M but imputed sex F', | |||
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the logic behind this change... ROS_006_18Y03227_D1 is now denoted as U in the test pedigree, so the family fails for only the 'Sample ROS_006_18Y03226_D1 has pedigree sex F but imputed sex M' reason.
| if family.samples[sample_id].sex not in { | ||
| sex_check_lookup[sample_id], | ||
| Sex.UNKNOWN, | ||
| }: # NB: Unknown samples in pedigree are excluded from sex check. |
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do we know what Unknowns look like in our DSP/GP friends' returns?
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remind me: so the sex_check_lookup is what our DSP/GP friends are delivering, right. So if a given sample is 'Unknown' in Seqr, it doesn't matter what it's returned as in our DSP/GP friends' metrics.tsv file thing.
Would we want to try and ensure that it's also returned as 'U' by them? But once again, I don't know how that would look like returned
This does still fail of the family.samples[sample_id].sex is M/F and sex_check_lookup[sample_id] is F/M, or vice-versa.
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I think my thinking on this was that a U in the pedigree is quite distinct from a U in the imputed sex file and that they aren't actually comparable. The former is a project management issue whereas the latter is likely a statistical issue within DRAGEN.
I don't actually know how a U would be delivered in the imputed sex file, so we were, on purpose, extremely strict with the import of that column.
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Heard! In that case, lgtm
| if family.samples[sample_id].sex not in { | ||
| sex_check_lookup[sample_id], | ||
| Sex.UNKNOWN, | ||
| }: # NB: Unknown samples in pedigree are excluded from sex check. |
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Heard! In that case, lgtm
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