QCAssessmentDepthBased

QCAssessmentDepthBased

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

  • bai (File, required): Index file for given bam file
  • bam (File, required): Bam file to assess
  • coverage_bed_file (File, required): Bed file for regions to assess
  • prefix (String, required): Prefix for output files
  • ref_map_file (File, required): Reference map file for the primary reference sequence and auxillary file locations.

Optional

  • t_001_CallableLoci.runtime_attr_override (RuntimeAttr?)
  • t_001_MosDepthOverBed.runtime_attr_override (RuntimeAttr?)
  • t_002_AssessQualityMetrics.runtime_attr_override (RuntimeAttr?)
  • t_003_FastQC.runtime_attr_override (RuntimeAttr?)

Defaults

  • min_callable_fraction (Float, default=0.5): Minimum required fraction of genome that is callable (default: 0.50)
  • min_coverage (Float, default=5): Minimum required mean coverage depth (default: 5)
  • min_coverage_threshold_regions (Float, default=0.2): Minimum required fraction of genome that must have a coverage depth greater than min_coverage (default: 0.2)
  • t_001_CallableLoci.min_base_quality (Int, default=20)
  • t_001_CallableLoci.min_mapping_quality (Int, default=10)
  • t_003_FastQC.num_cpus (Int, default=4)

Outputs

  • qc_status (String)
  • qc_message (String)
  • mosdepth_global_dist (File)
  • mosdepth_region_dist (File)
  • mosdepth_regions (File)
  • mosdepth_regions_csi (File)
  • callable_loci_summary (File)
  • callable_loci_bed (File)
  • fastqc_stats (File)
  • fastqc_report (File)

Dot Diagram

QCAssessmentDepthBased