CallVariantsIllumina

CallVariants

description
A workflow for calling small variants from an Illumina BAM file.

Inputs

Required

  • bai (File, required)
  • bam (File, required)
  • call_small_variants (Boolean, required)
  • prefix (String, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_fai (File, required)
  • run_dv_pepper_analysis (Boolean, required)
  • sample_id (String, required)

Optional

  • dvp_memory (Int?)
  • dvp_threads (Int?)
  • SmallVariantsScatterPrepp.runtime_attr_override (RuntimeAttr?)
  • DeepVariant.deep_variant.runtime_attr_override (RuntimeAttr?)

Defaults

  • call_small_vars_on_mitochondria (Boolean, default=true)
  • contigs_names_to_ignore (Array[String], default=["RANDOM_PLACEHOLDER_VALUE"])
  • mito_contig (String, default="chrM")
  • arbitrary.region (String, default="us-central1")

Outputs

  • dvp_g_vcf (File?)
  • dvp_g_tbi (File?)
  • dvp_vcf (File?)
  • dvp_tbi (File?)

Dot Diagram

CallVariantsIllumina