HaplotypeCaller

CallVariantsWithHaplotypeCaller

author
Jonn Smith
description
A workflow for calling small variants with GATK HaplotypeCaller from an Illumina BAM file.

Inputs

Required

  • bai (File, required)
  • bam (File, required)
  • dbsnp_vcf (File, required)
  • prefix (String, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_fai (File, required)
  • sample_id (String, required)

Optional

  • haplotype_caller_runtime_attr_override (RuntimeAttr?)
  • interval_list (File?)
  • CallVariantsWithHC.single_interval (String?)
  • CollapseGVCFtoVCF.runtime_attr_override (RuntimeAttr?)
  • CreateIntervalListFileFromIntervalInfo.runtime_attr_override (RuntimeAttr?)
  • ExtractIntervalNamesFromIntervalOrBamFile.runtime_attr_override (RuntimeAttr?)
  • IndexBamout.runtime_attr_override (RuntimeAttr?)
  • MergeGVCFs.runtime_attr_override (RuntimeAttr?)
  • MergeVariantCalledBamOuts.runtime_attr_override (RuntimeAttr?)
  • ReblockHcGVCF.annotations_to_keep (Array[String]?)
  • ReblockHcGVCF.runtime_attr_override (RuntimeAttr?)
  • ReblockHcGVCF.tree_score_cutoff (Float?)
  • SmallVariantsScatterPrep.runtime_attr_override (RuntimeAttr?)

Defaults

  • call_vars_on_mitochondria (Boolean, default=true)
  • contigs_names_to_ignore (Array[String], default=["RANDOM_PLACEHOLDER_VALUE"])
  • enable_pileup_mode (Boolean, default=false)
  • heterozygosity (Float, default=0.001)
  • heterozygosity_stdev (Float, default=0.01)
  • indel_heterozygosity (Float, default=0.000125)
  • mito_contig (String, default="chrM")
  • ploidy (Int, default=2)
  • CallVariantsWithHC.enable_dangling_branch_recovery (Boolean, default=false)
  • CollapseGVCFtoVCF.heterozygosity (Float, default=0.001)
  • CollapseGVCFtoVCF.heterozygosity_stdev (Float, default=0.01)
  • CollapseGVCFtoVCF.indel_heterozygosity (Float, default=0.000125)
  • CollapseGVCFtoVCF.keep_combined_raw_annotations (Boolean, default=false)
  • ReblockHcGVCF.gq_blocks (Array[Int], default=[20, 30, 40])

Outputs

  • output_gvcf (File)
  • output_gvcf_index (File)
  • output_vcf (File)
  • output_vcf_index (File)
  • bamout (File)
  • bamout_index (File)

Dot Diagram

HaplotypeCaller