PBSV

RunPBSV

description
Run PBSV to call SVs from a BAM file.

Inputs

Required

  • bai (File, required): index accompanying the BAM
  • bam (File, required): input BAM from which to call SVs
  • is_ccs (Boolean, required): if input BAM is CCS reads
  • prefix (String, required): prefix for output
  • ref_fasta (File, required): reference to which the BAM was aligned to
  • ref_fasta_fai (File, required): index accompanying the reference
  • zones (String, required): zones to run in

Optional

  • tandem_repeat_bed (File?): BED file containing TRF finder results (e.g. http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.trf.bed.gz)
  • Call.runtime_attr_override (RuntimeAttr?)
  • Discover.chr (String?)
  • Discover.runtime_attr_override (RuntimeAttr?)

Outputs

  • vcf (File)

Dot Diagram

PBSV