QCAssessment

AssessQualityMetrics

description
Assess quality metrics from mosdepth coverage and callable loci data to determine pass/fail status. To pass, the fraction of callable bases must be greater than min_callable_fraction and at least min_coverage_threshold_regions fraction of the genome must have a coverage depth greater than min_coverage.

Inputs

Required

  • callable_loci_summary (File, required): Summary file from GATK CallableLoci
  • mosdepth_region_bed (File, required): Region bed file from mosdepth
  • prefix (String, required): Prefix for output files

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • min_callable_fraction (Float, default=0.5): Minimum required fraction of genome that is callable
  • min_coverage (Float, default=5): Minimum required mean coverage depth
  • min_coverage_threshold_regions (Float, default=0.2): Minimum required fraction of genome that must have a coverage depth greater than min_coverage

Outputs

  • qc_status (String)
  • qc_message (String)