SampleLevelAlignedMetrics

SampleLevelAlignedMetrics

description
A utility (sub-)workflow to compute coverage on sample-leve BAM, and optionally over a provided BED file

Inputs

Required

  • aligned_bai (File, required): Index for the aligned BAM file
  • aligned_bam (File, required): Aligned BAM file
  • ref_fasta (File, required): Reference FASTA file

Optional

  • bed_to_compute_coverage (File?): Optional BED file to compute coverage over
  • ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • MosDepthOverBed.runtime_attr_override (RuntimeAttr?)
  • NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • cov_over_region.runtime_attr_override (RuntimeAttr?)

Outputs

  • bed_cov_summary (File?)
  • aligned_num_reads (Float)
  • aligned_num_bases (Float)
  • aligned_frac_bases (Float)
  • aligned_est_fold_cov (Float)
  • aligned_read_length_mean (Float)
  • aligned_read_length_median (Float)
  • aligned_read_length_stdev (Float)
  • aligned_read_length_N50 (Float)
  • average_identity (Float)
  • median_identity (Float)
  • reads_stats (Map[String,Float])

Dot Diagram

SampleLevelAlignedMetrics