Validate average coverage

Clinical-Genomics · Dec 12, 2023 · 72b3f99 · 72b3f99
1 parent 4cabeca
commit 72b3f99
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Showing 3 changed files with 12 additions and 0 deletions.
diff --git a/cg/constants/constants.py b/cg/constants/constants.py
@@ -211,6 +211,7 @@ class APIMethods(StrEnum):
 
 
 class MicrosaltQC:
+    AVERAGE_COVERAGE_THRESHOLD: int = 10
     QC_PERCENT_THRESHOLD_MWX: float = 0.1
     COVERAGE_10X_THRESHOLD: float = 0.75
     DUPLICATION_RATE_THRESHOLD: float = 0.8

diff --git a/cg/meta/workflow/microsalt/quality_checker.py b/cg/meta/workflow/microsalt/quality_checker.py
@@ -6,6 +6,7 @@
 from cg.constants.constants import MicrosaltAppTags, MicrosaltQC
 from cg.meta.workflow.microsalt.models import QualityMetrics, QualityResult, SampleMetrics
 from cg.meta.workflow.microsalt.utils import (
+    is_valid_average_coverage,
     is_valid_duplication_rate,
     is_valid_mapped_rate,
     is_valid_median_insert_size,
@@ -40,6 +41,8 @@ def quality_control_sample(self, sample_id: str, metrics: SampleMetrics) -> Qual
         valid_reads: bool = self.is_valid_total_reads(sample_id)
         valid_mapped_rate: bool = self.is_valid_mapped_rate(metrics)
         valid_duplication_rate: bool = self.is_valid_duplication_rate(metrics)
+        valid_median_insert_size: bool = self.is_valid_median_insert_size(metrics)
+        valid_average_coverage: bool = self.is_valid_average_coverage(metrics)
 
     def quality_control_case(self, sample_results: list[QualityResult]) -> bool:
         pass
@@ -171,3 +174,7 @@ def is_valid_duplication_rate(self, metrics: SampleMetrics) -> bool:
     def is_valid_median_insert_size(self, metrics: SampleMetrics) -> bool:
         insert_size: int = metrics.picard_markduplicate.insert_size
         return is_valid_median_insert_size(insert_size)
+
+    def is_valid_average_coverage(self, metrics: SampleMetrics) -> bool:
+        average_coverage: float = metrics.microsalt_samtools_stats.average_coverage
+        return is_valid_average_coverage(average_coverage)
diff --git a/cg/meta/workflow/microsalt/utils.py b/cg/meta/workflow/microsalt/utils.py
@@ -25,6 +25,10 @@ def is_valid_median_insert_size(sample_insert_size: int) -> bool:
     return sample_insert_size > MicrosaltQC.INSERT_SIZE_THRESHOLD
 
 
+def is_valid_average_coverage(average_coverage: float) -> bool:
+    return average_coverage > MicrosaltQC.AVERAGE_COVERAGE_THRESHOLD
+
+
 def parse_quality_metrics(file_path: Path) -> QualityMetrics:
     data = read_json(file_path)
     return QualityMetrics.model_validate_json(data)