AlignAndCheckFingerprintCCS

AlignAndCheckFingerprintCCS

desciption
Given an unaligned CCS/HiFi BAM for a sample, align and verify fingerprint.

Inputs

Required

  • bam_sample_name (String, required)
  • fp_store (String, required): Bucket name and prefix (gs://...) storing the fingerprinting VCFs
  • library (String, required)
  • ref_map_file (File, required)
  • sample_id_at_store (String, required): Name of the sample at the fingerprint store.
  • turn_off_fingperprint_check (Boolean, required): Please turn of fingerprint check if the reference is not GRCh38.
  • uBAM (File, required)
  • uPBI (File, required)

Optional

  • AlignReads.runtime_attr_override (RuntimeAttr?)
  • AlignReadsTogether.runtime_attr_override (RuntimeAttr?)
  • IndexAlignedReads.runtime_attr_override (RuntimeAttr?)
  • MergeAlignedReads.runtime_attr_override (RuntimeAttr?)
  • ShardLongReads.runtime_attr_override (RuntimeAttr?)
  • ValidateShard.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.SummarizeAlignedPBI.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.SummarizeAlignedQ10PBI.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.SummarizeAlignedQ12PBI.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.SummarizeAlignedQ15PBI.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.SummarizeAlignedQ5PBI.runtime_attr_override (RuntimeAttr?)
  • CollectPacBioAlignedMetrics.SummarizeAlignedQ7PBI.runtime_attr_override (RuntimeAttr?)
  • FPCheckAoU.CheckFingerprint.runtime_attr_override (RuntimeAttr?)
  • FPCheckAoU.ExtractRelevantGenotypingReads.runtime_attr_override (RuntimeAttr?)
  • FPCheckAoU.GetVCFSampleName.runtime_attr_override (RuntimeAttr?)
  • FPCheckAoU.ResolveFPVCFPath.runtime_attr_override (RuntimeAttr?)

Defaults

  • AlignReads.prefix (String, default="out")
  • AlignReadsTogether.prefix (String, default="out")
  • FPCheckAoU.lod_fail_threshold (Float, default=-3.0)
  • FPCheckAoU.lod_pass_threshold (Float, default=6.0)
  • ShardLongReads.drop_per_base_N_pulse_tags (Boolean, default=false)
  • ShardLongReads.num_threads (Int, default=8)
  • ShardLongReads.prefix (String, default="shard")
  • arbitrary.region (String, default="us-central1")
  • CollectPacBioAlignedMetrics.SummarizeAlignedPBI.qual_threshold (Int, default=0)
  • FPCheckAoU.FilterGenotypesVCF.filters (Array[String], default=['_random\t', '_decoy\t', '_alt\t', '^chrUn', '^HLA', '^EBV'])

Outputs

  • aligned_bam (File)
  • aligned_bai (File)
  • aligned_pbi (File)
  • alignment_metrics_tar_gz (File)
  • fp_lod_expected_sample (Float?)
  • fp_status (String?)
  • fingerprint_detail_tar_gz (File?)

Dot Diagram

AlignAndCheckFingerprintCCS