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 filebam
(File, required): Bam file to assesscoverage_bed_file
(File, required): Bed file for regions to assessprefix
(String, required): Prefix for output filesref_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)