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Support unknowns in pedigree #795

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Merged
merged 3 commits into from
May 28, 2024
Merged

Support unknowns in pedigree #795

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1f5e35f
exclude unknowns from sex check
bpblanken May 28, 2024
92dc012
add a test
bpblanken May 28, 2024
9436964
ruff
bpblanken May 28, 2024
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5 changes: 4 additions & 1 deletion v03_pipeline/lib/misc/family_loading_failures.py
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Expand Up @@ -175,7 +175,10 @@ def get_families_failed_sex_check(
failed_families = defaultdict(list)
for family in families:
for sample_id in family.samples:
if family.samples[sample_id].sex != sex_check_lookup[sample_id]:
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

failed_families[family].append(
f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but imputed sex {sex_check_lookup[sample_id].value}',
)
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1 change: 0 additions & 1 deletion v03_pipeline/lib/misc/family_loading_failures_test.py
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Expand Up @@ -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.

],
],
)
2 changes: 1 addition & 1 deletion v03_pipeline/lib/misc/pedigree_test.py
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Expand Up @@ -316,7 +316,7 @@ def test_parse_project(self) -> None:
samples={
'BBL_BC1-000345_01_D1': Sample(
sample_id='BBL_BC1-000345_01_D1',
sex=Sex.FEMALE,
sex=Sex.UNKNOWN,
mother='BBL_BC1-000345_03_D1',
father='BBL_BC1-000345_02_D1',
maternal_grandmother=None,
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1 change: 1 addition & 0 deletions v03_pipeline/lib/model/definitions.py
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Expand Up @@ -11,6 +11,7 @@ class AccessControl(Enum):
class Sex(Enum):
FEMALE = 'F'
MALE = 'M'
UNKNOWN = 'U'


class PipelineVersion(Enum):
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2 changes: 1 addition & 1 deletion v03_pipeline/var/test/pedigrees/test_pedigree_2.tsv
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Expand Up @@ -6,6 +6,6 @@ R0111_tgg_bblanken_wes BBL_HT-007-5195_1 BBL_HT-007-5195 BBL_HT-007-5195_03_D1
R0111_tgg_bblanken_wes BBL_HT-007-5195_1 BBL_HT-007-5195 BBL_HT-007-5195_04_D1 BBL_HT-007-5195_02_D1 BBL_HT-007-5195_03_D1 M
R0111_tgg_bblanken_wes BBL_HT-007-5195_1 BBL_HT-007-5195 BBL_HT-007-5195_05_D1 BBL_HT-007-5195_02_D1 BBL_HT-007-5195_03_D1 F
R0111_tgg_bblanken_wes BBL_HT-007-5195_1 BBL_HT-007-5195 BBL_HT-007-5195_06_D1 BBL_HT-007-5195_02_D1 BBL_HT-007-5195_03_D1 M
R0111_tgg_bblanken_wes BBL_BC1-000345_1 BBL_BC1-000345 BBL_BC1-000345_01_D1 BBL_BC1-000345_02_D1 BBL_BC1-000345_03_D1 F
R0111_tgg_bblanken_wes BBL_BC1-000345_1 BBL_BC1-000345 BBL_BC1-000345_01_D1 BBL_BC1-000345_02_D1 BBL_BC1-000345_03_D1 U
R0111_tgg_bblanken_wes BBL_BC1-000345_1 BBL_BC1-000345 BBL_BC1-000345_02_D1 M
R0111_tgg_bblanken_wes BBL_BC1-000345_1 BBL_BC1-000345 BBL_BC1-000345_03_D1 F
2 changes: 1 addition & 1 deletion v03_pipeline/var/test/pedigrees/test_pedigree_6.tsv
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@@ -1,6 +1,6 @@
Project_GUID Family_GUID Family_ID Individual_ID Paternal_ID Maternal_ID Sex
R0116_sex_check_project2 family_1 family_1 ROS_006_18Y03226_D1 F
R0116_sex_check_project2 family_1 family_1 ROS_006_18Y03227_D1 M
R0116_sex_check_project2 family_1 family_1 ROS_006_18Y03227_D1 U
R0116_sex_check_project2 family_1 family_1 ROS_006_18Y03228_D1 ROS_006_18Y03226_D1 ROS_006_18Y03227_D1 F
R0116_sex_check_project2 family_2 family_2 ROS_007_19Y05919_D1 F
R0116_sex_check_project2 family_2 family_2 ROS_007_19Y05939_D1 F
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