comments

Author: jklugherz

v03_pipeline/lib/methods/sample_qc.py

@@ -1,8 +1,12 @@
 import hail as hl
 from gnomad.sample_qc.pipeline import filter_rows_for_qc
 
+from v03_pipeline.lib.misc.terra_data_repository import BIGQUERY_METRICS
 from v03_pipeline.lib.model import SampleType
 
+GNOMAD_FILTER_MIN_AF = 0.001
+GNOMAD_FILTER_MIN_CALLRATE = 0.99
+
 CALLRATE_LOW_THRESHOLD = 0.85
 CONTAMINATION_UPPER_THRESHOLD = 5
 WES_COVERAGE_LOW_THRESHOLD = 85
@@ -14,7 +18,6 @@ def call_sample_qc(
     tdr_metrics_ht: hl.Table,
     sample_type: SampleType,
 ):
-    mt = mt.annotate_cols(sample_type=sample_type)
     mt = mt.annotate_entries(
         GT=hl.case()
         .when(mt.GT.is_diploid(), hl.call(mt.GT[0], mt.GT[1], phased=False))
@@ -28,8 +31,8 @@ def call_sample_qc(
 def annotate_filtered_callrate(mt: hl.MatrixTable) -> hl.MatrixTable:
     filtered_mt = filter_rows_for_qc(
         mt,
-        min_af=0.001,
-        min_callrate=0.99,
+        min_af=GNOMAD_FILTER_MIN_AF,
+        min_callrate=GNOMAD_FILTER_MIN_CALLRATE,
         bi_allelic_only=True,
         snv_only=True,
         apply_hard_filters=False,
@@ -62,8 +65,6 @@ def annotate_filter_flags(
             [hl.or_missing(filter_cond, name) for name, filter_cond in flags.items()],
         ).filter(hl.is_defined),
     ).drop(
-        'contamination_rate',
-        'percent_bases_at_20x',
-        'mean_coverage',
+        *BIGQUERY_METRICS[2:5],
         'filtered_callrate',
     )

v03_pipeline/lib/tasks/write_metadata_for_run_test.py

@@ -96,19 +96,10 @@ def test_write_metadata_for_run_task(
                         TEST_VCF,
                     ),
                     'sample_qc': {
-                        'HG00731': {
-                            'sample_type': 'WGS',
-                            'filter_flags': ['coverage', 'contamination'],
-                        },
-                        'HG00732': {
-                            'sample_type': 'WGS',
-                            'filter_flags': ['coverage'],
-                        },
-                        'HG00733': {
-                            'sample_type': 'WGS',
-                            'filter_flags': ['contamination'],
-                        },
-                        'NA19675': {'sample_type': 'WGS', 'filter_flags': []},
+                        'HG00731': {'filter_flags': ['coverage', 'contamination']},
+                        'HG00732': {'filter_flags': ['coverage']},
+                        'HG00733': {'filter_flags': ['contamination']},
+                        'NA19675': {'filter_flags': []},
                     },
                 },
             )

v03_pipeline/lib/tasks/write_sample_qc_json_test.py

@@ -47,23 +47,17 @@ def test_call_sample_qc(
 
         self.assertCountEqual(
             res['HG00731'],
-            {
-                'sample_type': 'WGS',
-                'filter_flags': ['contamination', 'coverage'],
-            },
+            {'filter_flags': ['contamination', 'coverage']},
         )
         self.assertCountEqual(
             res['HG00732'],
-            {'sample_type': 'WGS', 'filter_flags': ['coverage']},
+            {'filter_flags': ['coverage']},
         )
         self.assertCountEqual(
             res['HG00733'],
-            {
-                'sample_type': 'WGS',
-                'filter_flags': ['contamination'],
-            },
+            {'filter_flags': ['contamination']},
         )
         self.assertCountEqual(
             res['HG00732'],
-            {'sample_type': 'WGS', 'filter_flags': []},
+            {'filter_flags': []},
         )

v03_pipeline/var/test/sample_qc_1.json

@@ -1 +1 @@
-{"HG00731": {"sample_type": "WGS", "filter_flags": ["coverage", "contamination"]}, "HG00732": {"sample_type": "WGS", "filter_flags": ["coverage"]}, "HG00733": {"sample_type": "WGS", "filter_flags": ["contamination"]}, "NA19675": {"sample_type": "WGS", "filter_flags": []}}
+{"HG00731": {"filter_flags": ["coverage", "contamination"]}, "HG00732": {"filter_flags": ["coverage"]}, "HG00733": {"filter_flags": ["contamination"]}, "NA19675": {"filter_flags": []}}