Clair

Clair

description
Call variants using Clair3.

Inputs

Required

  • bai (File, required): index accompanying the BAM
  • bam (File, required): input BAM from which to call variants
  • preset (String, required): calling preset (CCS, ONT)
  • ref_fasta (File, required): reference to which the BAM was aligned to
  • ref_fasta_fai (File, required): index accompanying the reference
  • zone_string (String, required): zones to run the task on

Optional

  • chr (String?): chr on which to call variants
  • runtime_attr_override (RuntimeAttr?): override the default runtime attributes
  • sites_vcf (File?): sites VCF
  • sites_vcf_tbi (File?): sites VCF index

Outputs

  • pileup_vcf (File?)
  • pileup_vcf_tbi (File?)
  • full_alignment_vcf (File?)
  • full_alignment_tbi (File?)
  • vcf (File)
  • vcf_tbi (File?)
  • gvcf (File)
  • gvcf_tbi (File?)