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FilterBatch

Filters poor quality variants and filters outlier samples. This workflow can be run all at once with the WDL at wdl/FilterBatch.wdl, or it can be run in three steps to enable tuning of outlier filtration cutoffs. The three subworkflows are:

  1. FilterBatchSites: Per-batch variant filtration

  2. PlotSVCountsPerSample: Visualize SV counts per sample per type to help choose an IQR cutoff for outlier filtering, and preview outlier samples for a given cutoff

  3. FilterBatchSamples: Per-batch outlier sample filtration; provide an appropriate outlier_cutoff_nIQR based on the SV count plots and outlier previews from step 2. Note that not removing high outliers can result in increased compute cost and a higher false positive rate in later steps.

Prerequisites​

  • Generate Batch Metrics

Inputs​

  • Batch PED file
  • Metrics file (GenerateBatchMetrics)
  • Clustered SV and depth-only call VCFs (ClusterBatch)

Outputs​

  • Filtered SV (non-depth-only a.k.a. "PESR") VCF with outlier samples excluded
  • Filtered depth-only call VCF with outlier samples excluded
  • Random forest cutoffs file
  • PED file with outlier samples excluded