FPCheckAoU

FPCheckAoU

description
Check correctness of metadata on a (demultiplexed) alignmed BAM, by genotyping it's BAM generated with its metadata, against a fingerprint VCF. Practically assumes human GRCh38 reference.

Inputs

Required

  • aligned_bai (File, required)
  • aligned_bam (File, required): GCS path to aligned BAM file, supposed to be of the same sample as from the fingerprinting (FP) VCF
  • fp_store (String, required): Name of the bucket and prefix holding the fingerprint VCFs.
  • ref_specific_haplotype_map (File, required): Happlotype map file for the reference build used. See https://bit.ly/3QyZbwt
  • sample_id_at_store (String, required): UUID of the sample at the fingerprint store, used to fetch the fingerprinting VCF

Optional

  • CheckFingerprint.runtime_attr_override (RuntimeAttr?)
  • ExtractRelevantGenotypingReads.runtime_attr_override (RuntimeAttr?)
  • GetVCFSampleName.runtime_attr_override (RuntimeAttr?)
  • ResolveFPVCFPath.runtime_attr_override (RuntimeAttr?)

Defaults

  • lod_fail_threshold (Float, default=-3.0): A numeric threshold for LOD below which the sample will be considered failing the FP check.
  • lod_pass_threshold (Float, default=6.0): A numeric threshold for LOD above which the sample will be considered passing the FP check.
  • FilterGenotypesVCF.filters (Array[String], default=['_random\t', '_decoy\t', '_alt\t', '^chrUn', '^HLA', '^EBV'])

Outputs

  • lod_expected_sample (Float)
  • FP_status (String)
  • fingerprint_summary (File)
  • fingerprint_details (File)

Dot Diagram

FPCheckAoU