FindBamIdentity

FindBamIdentity

description
A workflow to identify a flowcell's the true identity, by genotyping it's BAM, against an array of 'truth' genotyped VCF.

Inputs

Required

  • aligned_bai (File, required)
  • aligned_bam (File, required): GCS path to aligned BAM file of the flowcell
  • expt_type (String, required): There will be special treatment for 'CLR' data (minimum base quality for bases used when computing a fingerprint)
  • fingerprint_store (String, required): GS path to where all known fingerprinting GT'ed VCFS are stored
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • vcf_filter_expression (String?): an expression used for picking up VCFs, the filter will be applied to VCF names, any match will lead to the VCF to be included
  • CheckCLRFingerprint.runtime_attr_override (RuntimeAttr?)
  • CheckFingerprint.runtime_attr_override (RuntimeAttr?)
  • ExtractRelevantGenotypingReads.runtime_attr_override (RuntimeAttr?)
  • GetVCFSampleName.runtime_attr_override (RuntimeAttr?)
  • ResetCLRBaseQual.runtime_attr_override (RuntimeAttr?)

Defaults

  • artificial_baseQ_for_CLR (Int, default=10): An artificial value for CLR reads used for fingerprint verification (CLR reads come with all 0 base qual)
  • FilterGenotypesVCF.filters (Array[String], default=['_random\t', '_decoy\t', '_alt\t', '^chrUn', '^HLA', '^EBV'])

Outputs

  • lod (Float)
  • true_smid (String)
  • true_collab_sample_id (String)
  • true_collab_partic_id (String)

Dot Diagram

FindBamIdentity