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Support unknown in predicted sex (#900)
* Support unknown * tests pass * Support Unknown in the reported sex column * add log * ruff * fix comma
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-30
lines changed

7 files changed

+51
-30
lines changed

‎v03_pipeline/lib/misc/family_loading_failures.py

Lines changed: 15 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,14 @@
33
import hail as hl
44
import numpy as np
55

6+
from v03_pipeline.lib.logger import get_logger
67
from v03_pipeline.lib.misc.pedigree import Family, Relation, Sample
78
from v03_pipeline.lib.model import Sex
89

910
RELATEDNESS_TOLERANCE = 0.2
1011

12+
logger = get_logger(__name__)
13+
1114

1215
def passes_relatedness_check(
1316
relatedness_check_lookup: dict[tuple[str, str], list],
@@ -175,10 +178,18 @@ def get_families_failed_sex_check(
175178
failed_families = defaultdict(list)
176179
for family in families:
177180
for sample_id in family.samples:
178-
if family.samples[sample_id].sex not in {
179-
sex_check_lookup[sample_id],
180-
Sex.UNKNOWN,
181-
}: # NB: Unknown samples in pedigree are excluded from sex check.
181+
# NB: Both Unknown samples in pedigree and Unknown
182+
# samples in the predicted_sex are precluded from
183+
# failing the sex check.
184+
if (
185+
sex_check_lookup[sample_id] == Sex.UNKNOWN # noqa: PLR1714
186+
or family.samples[sample_id].sex == Sex.UNKNOWN
187+
):
188+
logger.info(
189+
f'Encountered sample with Unknown sex excluded from sex check: {sample_id}',
190+
)
191+
192+
if family.samples[sample_id].sex != sex_check_lookup[sample_id]:
182193
failed_families[family].append(
183194
f'Sample {sample_id} has pedigree sex {family.samples[sample_id].sex.value} but imputed sex {sex_check_lookup[sample_id].value}',
184195
)

‎v03_pipeline/lib/misc/family_loading_failures_test.py

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -56,12 +56,12 @@ def test_build_relatedness_check_lookup(self):
5656
def test_build_sex_check_lookup(self):
5757
ht = hl.Table.parallelize(
5858
[
59-
{'s': 'remapped_id', 'predicted_sex': 'M'},
60-
{'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'M'},
61-
{'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'M'},
62-
{'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'M'},
63-
{'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'F'},
64-
{'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'M'},
59+
{'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'},
60+
{'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'},
61+
{'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'},
62+
{'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'},
63+
{'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'},
64+
{'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'},
6565
],
6666
hl.tstruct(
6767
s=hl.tstr,
@@ -72,12 +72,12 @@ def test_build_sex_check_lookup(self):
7272
self.assertEqual(
7373
build_sex_check_lookup(ht, hl.dict({'ROS_006_18Y03226_D1': 'remapped_id'})),
7474
{
75-
'remapped_id': Sex.MALE,
76-
'ROS_006_18Y03227_D1': Sex.MALE,
77-
'ROS_006_18Y03228_D1': Sex.MALE,
78-
'ROS_007_19Y05919_D1': Sex.MALE,
79-
'ROS_007_19Y05939_D1': Sex.FEMALE,
80-
'ROS_007_19Y05987_D1': Sex.MALE,
75+
'remapped_id': Sex.FEMALE,
76+
'ROS_006_18Y03227_D1': Sex.FEMALE,
77+
'ROS_006_18Y03228_D1': Sex.FEMALE,
78+
'ROS_007_19Y05919_D1': Sex.FEMALE,
79+
'ROS_007_19Y05939_D1': Sex.MALE,
80+
'ROS_007_19Y05987_D1': Sex.UNKNOWN,
8181
},
8282
)
8383

@@ -178,12 +178,12 @@ def test_all_relatedness_checks(self):
178178
def test_get_families_failed_sex_check(self):
179179
sex_check_ht = hl.Table.parallelize(
180180
[
181-
{'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'M'},
182-
{'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'},
181+
{'s': 'ROS_006_18Y03226_D1', 'predicted_sex': 'F'},
182+
{'s': 'ROS_006_18Y03227_D1', 'predicted_sex': 'F'}, # Pedigree Sex U
183183
{'s': 'ROS_006_18Y03228_D1', 'predicted_sex': 'F'},
184184
{'s': 'ROS_007_19Y05919_D1', 'predicted_sex': 'F'},
185-
{'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'F'},
186-
{'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'F'},
185+
{'s': 'ROS_007_19Y05939_D1', 'predicted_sex': 'M'},
186+
{'s': 'ROS_007_19Y05987_D1', 'predicted_sex': 'U'}, # Pedigree Sex F
187187
],
188188
hl.tstruct(
189189
s=hl.tstr,
@@ -201,7 +201,7 @@ def test_get_families_failed_sex_check(self):
201201
failed_families.values(),
202202
[
203203
[
204-
'Sample ROS_006_18Y03226_D1 has pedigree sex F but imputed sex M',
204+
'Sample ROS_007_19Y05939_D1 has pedigree sex F but imputed sex M',
205205
],
206206
],
207207
)

‎v03_pipeline/lib/misc/io.py

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -19,9 +19,6 @@
1919
MB_PER_PARTITION = 128
2020
MAX_SAMPLES_SPLIT_MULTI_SHUFFLE = 100
2121

22-
MALE = 'Male'
23-
FEMALE = 'Female'
24-
2522

2623
def validated_hl_function(
2724
regex_to_msg: dict[str, str | Template],
@@ -216,12 +213,17 @@ def select_relevant_fields(
216213

217214
def import_imputed_sex(imputed_sex_path: str) -> hl.Table:
218215
ht = hl.import_table(imputed_sex_path)
216+
imputed_sex_lookup = hl.dict(
217+
{s.imputed_sex_value: s.value for s in Sex},
218+
)
219219
ht = ht.select(
220220
s=ht.collaborator_sample_id,
221221
predicted_sex=(
222222
hl.case()
223-
.when(ht.predicted_sex == FEMALE, Sex.FEMALE.value)
224-
.when(ht.predicted_sex == MALE, Sex.MALE.value)
223+
.when(
224+
imputed_sex_lookup.contains(ht.predicted_sex),
225+
imputed_sex_lookup[ht.predicted_sex],
226+
)
225227
.or_error(
226228
hl.format(
227229
'Found unexpected value %s in imputed sex file',

‎v03_pipeline/lib/misc/io_test.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -45,15 +45,15 @@ def test_import_imputed_sex(self) -> None:
4545
[
4646
hl.Struct(s='abc_1', predicted_sex='M'),
4747
hl.Struct(s='abc_2', predicted_sex='F'),
48-
hl.Struct(s='abc_3', predicted_sex='M'),
48+
hl.Struct(s='abc_3', predicted_sex='U'),
4949
],
5050
)
5151

5252
def test_import_imputed_sex_unexpected_value(self) -> None:
5353
ht = import_imputed_sex(TEST_IMPUTED_SEX_UNEXPECTED_VALUE)
5454
self.assertRaisesRegex(
5555
hl.utils.java.HailUserError,
56-
'Found unexpected value Unknown in imputed sex file',
56+
'Found unexpected value UNKNOWN in imputed sex file',
5757
ht.collect,
5858
)
5959

‎v03_pipeline/lib/model/definitions.py

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -13,6 +13,14 @@ class Sex(str, Enum):
1313
MALE = 'M'
1414
UNKNOWN = 'U'
1515

16+
@property
17+
def imputed_sex_value(self):
18+
return {
19+
Sex.MALE: 'Male',
20+
Sex.FEMALE: 'Female',
21+
Sex.UNKNOWN: 'Unknown',
22+
}[self]
23+
1624

1725
class PipelineVersion(str, Enum):
1826
V02 = 'v02'

‎v03_pipeline/var/test/sex_check/test_imputed_sex.tsv

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
entity:sample_id collaborator_participant_id collaborator_sample_id contamination_rate coverage_region_1_metrics_file crai_path cram_md5_path cram_path datarepo_row_id dragen_version import:snapshot_id import:timestamp mapped_percentage mapping_metrics_file material_type mean_coverage original_material_type participant_id pass_fail_value pdo percent_bases_at_20x percent_callability predicted_sex product receipt_date reported_sex research_project single_sample_vcf_index_path single_sample_vcf_md5_path single_sample_vcf_path total_bases variant_calling_metrics_file
22
SM-DM66X abc_1 abc_1 0E+00 gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/6f30a41f-1d91-44d1-915c-5c10c6d87fcd/WAL_LIS6100_LIS6101.qc-coverage-region-1_coverage_metrics.csv gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/3e204a66-f044-4bdc-ade4-1671a0269214/WAL_LIS6100_LIS6101.cram.crai gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/a6ed4850-6a69-412e-a071-bf8cce04fca0/WAL_LIS6100_LIS6101.cram.md5sum gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/c51bbfd6-42f0-40ca-aa0c-b5eece935516/WAL_LIS6100_LIS6101.cram 8a07ce00-16a1-40f4-8666-c4cfaad1bbe1 07.021.604.3.7.8 cc9d9ed9-785a-407d-910e-d9bd46936fa6 2024-04-17T14:58:10 98.450000000 gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/9e745b1d-2c00-44ce-bbfb-31c44369f4fe/WAL_LIS6100_LIS6101.mapping_metrics.csv DNA:DNA Genomic 35.730000000 Whole Blood:Whole Blood PT-24FB4 Pass PDO-32851 96.140000000 97.850000000 Male P-WG-0139 2017-03-15 04:00:00 Male RP-3071 gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/360ec721-0af8-4085-a677-38c018069559/WAL_LIS6100_LIS6101.vcf.gz.tbi gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/8da8cda2-497f-4a8b-a642-af4a4ad28aac/WAL_LIS6100_LIS6101.vcf.gz.md5sum gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/0a2d93fb-8837-4b6f-ac68-a6b9701f9a08/WAL_LIS6100_LIS6101.vcf.gz 134324623400.000000000 gs://datarepo-9cafeffd-bucket/f511b131-3f0d-4eb7-a7f0-b2b3d73dca3a/f7b62337-1339-4c2e-8280-281c48604e07/WAL_LIS6100_LIS6101.vc_metrics.csv
33
SM-DM69X abc_2 abc_2 0E+00 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c4c07edf-7735-4aa7-9283-7cb2607b60a2/GLE-5774-3-3.qc-coverage-region-1_coverage_metrics.csv gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/dcd4c271-0249-47f1-8e91-81f74735c5a1/GLE-5774-3-3.cram.crai gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/ec41ec06-673f-4fe2-a063-23dc5fe1dcce/GLE-5774-3-3.cram.md5sum gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/aad0e270-2ad5-4f39-b968-9b4beafeb5cc/GLE-5774-3-3.cram a4b04a39-9234-4028-a155-442c4acf12a0 07.021.604.3.7.8 ce74d94c-c33d-49d7-85c9-5f3cbd08aff7 2024-04-17T15:02:46 99.800000000 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c3a9e6f2-4c68-410b-823d-46ca406e5061/GLE-5774-3-3.mapping_metrics.csv DNA:DNA Genomic 35.300000000 Whole Blood:Whole Blood PT-24OHM Pass PDO-32755 96.320000000 97.340000000 Female P-WG-0139 2017-04-12 04:00:00 Female RP-3061 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c71cd2a1-c789-4715-9ebc-dbfc40d9f2e2/GLE-5774-3-3.vcf.gz.tbi gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/957a99cb-c9a9-4fc5-a0ec-53f9e461469e/GLE-5774-3-3.vcf.gz.md5sum gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/df520949-5f2b-4976-9d46-80d1cc299813/GLE-5774-3-3.vcf.gz 133253714921.000000000 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/2e98e51b-9394-4e64-977f-e9010a4e16dc/GLE-5774-3-3.vc_metrics.csv
4-
SM-DPB5G abc_3 abc_3 0E+00 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/432f8354-77e0-4381-9bb5-dfdc0633b5b2/PIE_OGI1433_002628_1.qc-coverage-region-1_coverage_metrics.csv gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/3dc623fa-2a45-4b3d-a0f8-fcdec09f9418/PIE_OGI1433_002628_1.cram.crai gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/895966ef-c705-4c18-952d-03863243a184/PIE_OGI1433_002628_1.cram.md5sum gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/96ca6d5f-fb23-4102-bb5e-c7bbfd194e1c/PIE_OGI1433_002628_1.cram ffb50687-165e-425a-a545-c3797d3a28d4 07.021.604.3.7.8 55729ba9-3ce4-47b3-9c3b-1148737ae40f 2024-04-17T15:07:57 99.670000000 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/30f8e208-5d2d-4ce8-b835-695b5ed673f4/PIE_OGI1433_002628_1.mapping_metrics.csv DNA:DNA Genomic 41.910000000 Whole Blood:Whole Blood PT-25BR5 Pass PDO-32756 92.920000000 97.990000000 Male P-WG-0139 2017-05-19 04:00:00 Male RP-3062 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/1641d1b2-1035-4cc3-9c8b-0c8cb430f56b/PIE_OGI1433_002628_1.vcf.gz.tbi gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/f5ba2708-899e-42e8-b287-fdf72c2e404d/PIE_OGI1433_002628_1.vcf.gz.md5sum gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/e925ee5d-a75e-471f-adfd-2756c8690069/PIE_OGI1433_002628_1.vcf.gz 156149580126.000000000 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/df076bc5-9db8-44f0-a3fe-f693370634cc/PIE_OGI1433_002628_1.vc_metrics.csv
4+
SM-DPB5G abc_3 abc_3 0E+00 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/432f8354-77e0-4381-9bb5-dfdc0633b5b2/PIE_OGI1433_002628_1.qc-coverage-region-1_coverage_metrics.csv gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/3dc623fa-2a45-4b3d-a0f8-fcdec09f9418/PIE_OGI1433_002628_1.cram.crai gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/895966ef-c705-4c18-952d-03863243a184/PIE_OGI1433_002628_1.cram.md5sum gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/96ca6d5f-fb23-4102-bb5e-c7bbfd194e1c/PIE_OGI1433_002628_1.cram ffb50687-165e-425a-a545-c3797d3a28d4 07.021.604.3.7.8 55729ba9-3ce4-47b3-9c3b-1148737ae40f 2024-04-17T15:07:57 99.670000000 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/30f8e208-5d2d-4ce8-b835-695b5ed673f4/PIE_OGI1433_002628_1.mapping_metrics.csv DNA:DNA Genomic 41.910000000 Whole Blood:Whole Blood PT-25BR5 Pass PDO-32756 92.920000000 97.990000000 Unknown P-WG-0139 2017-05-19 04:00:00 Unknown RP-3062 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/1641d1b2-1035-4cc3-9c8b-0c8cb430f56b/PIE_OGI1433_002628_1.vcf.gz.tbi gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/f5ba2708-899e-42e8-b287-fdf72c2e404d/PIE_OGI1433_002628_1.vcf.gz.md5sum gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/e925ee5d-a75e-471f-adfd-2756c8690069/PIE_OGI1433_002628_1.vcf.gz 156149580126.000000000 gs://datarepo-c41dc160-bucket/907593be-8862-4945-9e70-f758b6448b8d/df076bc5-9db8-44f0-a3fe-f693370634cc/PIE_OGI1433_002628_1.vc_metrics.csv

‎v03_pipeline/var/test/sex_check/test_imputed_sex_unexpected_value.tsv

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,2 +1,2 @@
11
entity:sample_id collaborator_participant_id collaborator_sample_id contamination_rate coverage_region_1_metrics_file crai_path cram_md5_path cram_path datarepo_row_id dragen_version import:snapshot_id import:timestamp mapped_percentage mapping_metrics_file material_type mean_coverage original_material_type participant_id pass_fail_value pdo percent_bases_at_20x percent_callability predicted_sex product receipt_date reported_sex research_project single_sample_vcf_index_path single_sample_vcf_md5_path single_sample_vcf_path total_bases variant_calling_metrics_file
2-
SM-DM69X abc_2 abc_2 0E+00 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c4c07edf-7735-4aa7-9283-7cb2607b60a2/GLE-5774-3-3.qc-coverage-region-1_coverage_metrics.csv gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/dcd4c271-0249-47f1-8e91-81f74735c5a1/GLE-5774-3-3.cram.crai gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/ec41ec06-673f-4fe2-a063-23dc5fe1dcce/GLE-5774-3-3.cram.md5sum gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/aad0e270-2ad5-4f39-b968-9b4beafeb5cc/GLE-5774-3-3.cram a4b04a39-9234-4028-a155-442c4acf12a0 07.021.604.3.7.8 ce74d94c-c33d-49d7-85c9-5f3cbd08aff7 2024-04-17T15:02:46 99.800000000 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c3a9e6f2-4c68-410b-823d-46ca406e5061/GLE-5774-3-3.mapping_metrics.csv DNA:DNA Genomic 35.300000000 Whole Blood:Whole Blood PT-24OHM Pass PDO-32755 96.320000000 97.340000000 Unknown P-WG-0139 2017-04-12 04:00:00 Unknown RP-3061 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c71cd2a1-c789-4715-9ebc-dbfc40d9f2e2/GLE-5774-3-3.vcf.gz.tbi gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/957a99cb-c9a9-4fc5-a0ec-53f9e461469e/GLE-5774-3-3.vcf.gz.md5sum gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/df520949-5f2b-4976-9d46-80d1cc299813/GLE-5774-3-3.vcf.gz 133253714921.000000000 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/2e98e51b-9394-4e64-977f-e9010a4e16dc/GLE-5774-3-3.vc_metrics.csv
2+
SM-DM69X abc_2 abc_2 0E+00 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c4c07edf-7735-4aa7-9283-7cb2607b60a2/GLE-5774-3-3.qc-coverage-region-1_coverage_metrics.csv gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/dcd4c271-0249-47f1-8e91-81f74735c5a1/GLE-5774-3-3.cram.crai gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/ec41ec06-673f-4fe2-a063-23dc5fe1dcce/GLE-5774-3-3.cram.md5sum gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/aad0e270-2ad5-4f39-b968-9b4beafeb5cc/GLE-5774-3-3.cram a4b04a39-9234-4028-a155-442c4acf12a0 07.021.604.3.7.8 ce74d94c-c33d-49d7-85c9-5f3cbd08aff7 2024-04-17T15:02:46 99.800000000 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c3a9e6f2-4c68-410b-823d-46ca406e5061/GLE-5774-3-3.mapping_metrics.csv DNA:DNA Genomic 35.300000000 Whole Blood:Whole Blood PT-24OHM Pass PDO-32755 96.320000000 97.340000000 UNKNOWN P-WG-0139 2017-04-12 04:00:00 UNKNOWN RP-3061 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/c71cd2a1-c789-4715-9ebc-dbfc40d9f2e2/GLE-5774-3-3.vcf.gz.tbi gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/957a99cb-c9a9-4fc5-a0ec-53f9e461469e/GLE-5774-3-3.vcf.gz.md5sum gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/df520949-5f2b-4976-9d46-80d1cc299813/GLE-5774-3-3.vcf.gz 133253714921.000000000 gs://datarepo-556a9c15-bucket/2a4202b0-93f5-4ebe-8d2b-fd4cfb2b881d/2e98e51b-9394-4e64-977f-e9010a4e16dc/GLE-5774-3-3.vc_metrics.csv

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