ExtractRegionsFromBam

ExtractRegionsFromBam

desciption
Extract reads from the given bam file which overlap the regions in the given bed file.

Inputs

Required

  • extraction_comment (String, required): Comment to add to the end of the output filename.
  • gcs_bam_path (String, required): GCS URL to bam file from which to extract reads.
  • gcs_out_root_dir (String, required): Output folder into which to place the results of this workflow.
  • participant_name (String, required): Participant (or sample) name for the given bam file.
  • regions_bed (File, required): Bed file containing regions for which to extract reads.

Optional

  • Bam2Fastq.bam_index (File?)
  • Bam2Fastq.reference_dict (File?)
  • Bam2Fastq.reference_fasta (File?)
  • Bam2Fastq.reference_fasta_index (File?)
  • Bam2Fastq.runtime_attr_override (RuntimeAttr?)
  • FinalizeBai.keyfile (File?)
  • FinalizeBai.name (String?)
  • FinalizeBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeBam.keyfile (File?)
  • FinalizeBam.name (String?)
  • FinalizeBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeFqEnd1.keyfile (File?)
  • FinalizeFqEnd1.name (String?)
  • FinalizeFqEnd1.runtime_attr_override (RuntimeAttr?)
  • FinalizeFqEnd2.keyfile (File?)
  • FinalizeFqEnd2.name (String?)
  • FinalizeFqEnd2.runtime_attr_override (RuntimeAttr?)
  • FinalizeFqUnpaired.keyfile (File?)
  • FinalizeFqUnpaired.name (String?)
  • FinalizeFqUnpaired.runtime_attr_override (RuntimeAttr?)
  • GetReadsInBedFileRegions.runtime_attr_override (RuntimeAttr?)

Outputs

  • bam (File)
  • bai (File)
  • fq_end1 (File)
  • fq_end2 (File)
  • fq_unpaired (File)

Dot Diagram

ExtractRegionsFromBam