SvQCPlots

PlotSVQCMetrics

description
This workflow generates—for one or more samples—summaries and stats on the provided SV callers and their corresponding VCFs.

Inputs

Required

  • callers (Array[String], required): List of SV callers
  • cohort_name (String, required)
  • coverage_metrics (Array[Float], required): List of coverage metrics for each sample. Order must match the order of samples.
  • gcs_out_root_dir (String, required)
  • matching_vcfs (Array[Array[File]], required)
  • output_plot_notebook_name (String, required): Name of the output plot notebook
  • reference_name (String, required): Reference genome name
  • samples (Array[String], required): List of sample names. Order must match the order of coverage_metrics.

Optional

  • SaveHTML.keyfile (File?)
  • SaveHTML.name (String?)
  • SaveHTML.runtime_attr_override (RuntimeAttr?)
  • SaveNotebook.keyfile (File?)
  • SaveNotebook.runtime_attr_override (RuntimeAttr?)
  • SavePlotPDFs.keyfile (File?)
  • SavePlotPDFs.runtime_attr_override (RuntimeAttr?)
  • SaveStatsByCoverage.keyfile (File?)
  • SaveStatsByCoverage.runtime_attr_override (RuntimeAttr?)
  • SaveStatsBySVtype.keyfile (File?)
  • SaveStatsBySVtype.runtime_attr_override (RuntimeAttr?)
  • addCoverageToSVstats.runtime_attr_override (RuntimeAttr?)
  • bcfQuerySV.runtime_attr_override (RuntimeAttr?)
  • compileSVstats.runtime_attr_override (RuntimeAttr?)
  • concatSVstats.runtime_attr_override (RuntimeAttr?)
  • plotSVQCMetrics.runtime_attr_override (RuntimeAttr?)

Outputs

  • SvQCPlotsMisc (Map[String,String])
  • SvQCPlotsHTML (File)

Dot Diagram

SvQCPlots