Pf_Niare_HaplotypeCaller

CallVariantsWithHaplotypeCaller

author
Jonn Smith
description
A workflow for calling small variants with GATK HaplotypeCaller from an Illumina BAM file using the methods laid out by Niare et al. (https://doi.org/10.1186/s12936-023-04632-0).

Inputs

Required

  • bai (File, required): Input bam index for bam.
  • bam (File, required): Input bam file containing reads from which to call variants.
  • genotype_gvcfs_intervals (File, required)
  • prefix (String, required): Prefix to use for output files.
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_fai (File, required)
  • sample_id (String, required): ID of the sample being called.

Optional

  • CallVariantsWithHC.runtime_attr_override (RuntimeAttr?)
  • CollapseGVCFtoVCF.dbsnp_vcf (String?)
  • CollapseGVCFtoVCF.runtime_attr_override (RuntimeAttr?)
  • IndexBamout.runtime_attr_override (RuntimeAttr?)
  • MergeGVCFs.runtime_attr_override (RuntimeAttr?)
  • MergeVariantCalledBamOuts.runtime_attr_override (RuntimeAttr?)
  • SmallVariantsScatterPrep.runtime_attr_override (RuntimeAttr?)

Defaults

  • call_vars_on_mitochondria (Boolean, default=false): If true, will call variants on the mitochondrial contig.
  • contigs_names_to_ignore (Array[String], default=["RANDOM_PLACEHOLDER_VALUE"]): Array of names of contigs to ignore for the purposes of reporting variants.
  • mito_contig (String, default="chrM"): Name of the mitochondrial contig.
  • 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)
  • MergeGVCFs.is_gvcf (Boolean, default=false)

Outputs

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

Dot Diagram

Pf_Niare_HaplotypeCaller