SRWholeGenome_Pf_Niare_VQSR

SRWholeGenome_Pf_Niare_VQSR

author
Jonn Smith
description
This workflow replicates the single-sample pipeline from Niare et al. (https://doi.org/10.1186/s12936-023-04632-0) using LRMA conventions.

Inputs

Required

  • aligned_bais (Array[File], required): Array of aligned bam indices to process. Order must correspond to aligned_bams.
  • aligned_bams (Array[File], required): Array of aligned bam files to process.
  • gcs_out_root_dir (String, required): GCS Bucket into which to finalize outputs.
  • genotype_gvcfs_intervals (File, required): Intervals over which to batch Joint Genotyping.
  • participant_name (String, required): The unique identifier of this sample being processed.
  • ref_map_file (File, required): Reference map file indicating reference sequence and auxillary file locations
  • vcf_calling_interval_list (File, required): Intervals over which to call variants.
  • vqsr_sites_vcf (File, required): Sites-only VCF to use with VQSR for training.
  • vqsr_sites_vcf_index (File, required): VCF index of vqsr_sites_vcf

Optional

  • ApplyVqsrIndel.runtime_attr_override (RuntimeAttr?)
  • ApplyVqsrSnp.runtime_attr_override (RuntimeAttr?)
  • FinalizeHCBaiOut.name (String?)
  • FinalizeHCBaiOut.runtime_attr_override (RuntimeAttr?)
  • FinalizeHCBamOut.name (String?)
  • FinalizeHCBamOut.runtime_attr_override (RuntimeAttr?)
  • FinalizeHCGTbi.name (String?)
  • FinalizeHCGTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeHCGVcf.name (String?)
  • FinalizeHCGVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeRawHCTbi.name (String?)
  • FinalizeRawHCTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeRawHCVcf.name (String?)
  • FinalizeRawHCVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeRecalibratedVcf.name (String?)
  • FinalizeRecalibratedVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeRecalibratedVcfIndex.name (String?)
  • FinalizeRecalibratedVcfIndex.runtime_attr_override (RuntimeAttr?)
  • MergeAllReads.runtime_attr_override (RuntimeAttr?)
  • MergeMultiAllelicSitesPostRecalibration.runtime_attr_override (RuntimeAttr?)
  • NormalizeVcfPreVqsr.runtime_attr_override (RuntimeAttr?)
  • RenameRawHcGvcf.runtime_attr_override (RuntimeAttr?)
  • RenameRawHcVcf.runtime_attr_override (RuntimeAttr?)
  • SmallVariantsScatterPrep.runtime_attr_override (RuntimeAttr?)
  • VariantRecalibratorIndel.runtime_attr_override (RuntimeAttr?)
  • VariantRecalibratorSnp.runtime_attr_override (RuntimeAttr?)
  • CallVariantsWithHaplotypeCaller.CallVariantsWithHC.runtime_attr_override (RuntimeAttr?)
  • CallVariantsWithHaplotypeCaller.CollapseGVCFtoVCF.dbsnp_vcf (String?)
  • CallVariantsWithHaplotypeCaller.CollapseGVCFtoVCF.runtime_attr_override (RuntimeAttr?)
  • CallVariantsWithHaplotypeCaller.IndexBamout.runtime_attr_override (RuntimeAttr?)
  • CallVariantsWithHaplotypeCaller.MergeGVCFs.runtime_attr_override (RuntimeAttr?)
  • CallVariantsWithHaplotypeCaller.MergeVariantCalledBamOuts.runtime_attr_override (RuntimeAttr?)
  • CallVariantsWithHaplotypeCaller.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=["Pf3D7_API_v3"]): Array of names of contigs to ignore for the purposes of reporting variants.
  • mito_contig (String, default="Pf3D7_MIT_v3"): Name of the mitochondrial contig.
  • CallVariantsWithHaplotypeCaller.call_vars_on_mitochondria (Boolean, default=false): If true, will call variants on the mitochondrial contig.
  • NormalizeVcfPreVqsr.batch_size (Int, default=100)
  • RenameRawHcVcf.is_gvcf (Boolean, default=false)
  • CallVariantsWithHaplotypeCaller.CollapseGVCFtoVCF.heterozygosity (Float, default=0.001)
  • CallVariantsWithHaplotypeCaller.CollapseGVCFtoVCF.heterozygosity_stdev (Float, default=0.01)
  • CallVariantsWithHaplotypeCaller.CollapseGVCFtoVCF.indel_heterozygosity (Float, default=0.000125)
  • CallVariantsWithHaplotypeCaller.CollapseGVCFtoVCF.keep_combined_raw_annotations (Boolean, default=false)
  • CallVariantsWithHaplotypeCaller.MergeGVCFs.is_gvcf (Boolean, default=false)

Outputs

  • successfully_processed (Boolean)
  • hc_g_vcf (File?)
  • hc_g_tbi (File?)
  • hc_bamout (File?)
  • hc_baiout (File?)
  • hc_raw_vcf (File?)
  • hc_raw_tbi (File?)
  • hc_rescored_vcf (File?)
  • hc_rescored_tbi (File?)

Dot Diagram

SRWholeGenome_Pf_Niare_VQSR