AlignedMetrics

AlignedMetrics

description
Workflow to generate metrics for aligned BAMs

Inputs

Required

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

Optional

  • gcs_output_dir (String?): GCS Bucket into which to finalize outputs. If no bucket is given, outputs will not be finalized and instead will remain in their native execution location.
  • AlignedFlagStats.runtime_attr_override (RuntimeAttr?)
  • AlignedReadMetrics.runtime_attr_override (RuntimeAttr?)
  • FFCoverageFullDist.keyfile (File?)
  • FFCoverageFullDist.runtime_attr_override (RuntimeAttr?)
  • FFCoverageGlobalDist.keyfile (File?)
  • FFCoverageGlobalDist.runtime_attr_override (RuntimeAttr?)
  • FFCoverageQuantized.keyfile (File?)
  • FFCoverageQuantized.runtime_attr_override (RuntimeAttr?)
  • FFCoverageQuantizedCsi.keyfile (File?)
  • FFCoverageQuantizedCsi.runtime_attr_override (RuntimeAttr?)
  • FFCoverageQuantizedDist.keyfile (File?)
  • FFCoverageQuantizedDist.runtime_attr_override (RuntimeAttr?)
  • FFCoverageRegionDist.keyfile (File?)
  • FFCoverageRegionDist.runtime_attr_override (RuntimeAttr?)
  • FFCoverageRegions.keyfile (File?)
  • FFCoverageRegions.runtime_attr_override (RuntimeAttr?)
  • FFCoverageRegionsCsi.keyfile (File?)
  • FFCoverageRegionsCsi.runtime_attr_override (RuntimeAttr?)
  • FFDepthSummaries.keyfile (File?)
  • FFDepthSummaries.runtime_attr_override (RuntimeAttr?)
  • FFYieldAligned.keyfile (File?)
  • FFYieldAligned.runtime_attr_override (RuntimeAttr?)
  • MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • MosDepth.runtime_attr_override (RuntimeAttr?)
  • MosDepth.window_size (Int?)
  • SummarizeDepth.runtime_attr_override (RuntimeAttr?)

Outputs

  • aligned_flag_stats (File)
  • coverage_full_dist (Array[File])
  • coverage_global_dist (Array[File])
  • coverage_region_dist (Array[File])
  • coverage_regions (Array[File])
  • coverage_regions_csi (Array[File])
  • coverage_quantized_dist (Array[File])
  • coverage_quantized (Array[File])
  • coverage_quantized_csi (Array[File])
  • aligned_np_hist (File)
  • aligned_range_gap_hist (File)
  • aligned_zmw_hist (File)
  • aligned_prl_counts (File)
  • aligned_prl_hist (File)
  • aligned_prl_nx (File)
  • aligned_prl_yield_hist (File)
  • aligned_rl_counts (File)
  • aligned_rl_hist (File)
  • aligned_rl_nx (File)
  • aligned_rl_yield_hist (File)
  • raw_chr_intervals (File)

Dot Diagram

AlignedMetrics