SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR

SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR

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

Inputs

Required

  • gcs_out_root_dir (String, required): GCS Bucket into which to finalize outputs.
  • gvcf_indices (Array[File], required): Array of gvcf index files for gvcfs. Order should correspond to that in gvcfs.
  • gvcfs (Array[File], required): Array of GVCF files to use as inputs for joint calling.
  • prefix (String, required): Prefix to use for output files.
  • ref_map_file (File, required): Reference map file indicating reference sequence and auxillary file locations.
  • 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
  • SplitContigToIntervals.prefix (String, required): Prefix to use for output files.
  • SplitContigToIntervals.ref_fasta (File, required)
  • SplitContigToIntervals.ref_fasta_fai (File, required)

Optional

  • ApplyVqsrIndel.runtime_attr_override (RuntimeAttr?)
  • ApplyVqsrSnp.runtime_attr_override (RuntimeAttr?)
  • CreateSampleNameMap.runtime_attr_override (RuntimeAttr?)
  • FinalizeVETSTBI.name (String?)
  • FinalizeVETSTBI.runtime_attr_override (RuntimeAttr?)
  • FinalizeVETSVCF.name (String?)
  • FinalizeVETSVCF.runtime_attr_override (RuntimeAttr?)
  • GatherRescoredVcfs.runtime_attr_override (RuntimeAttr?)
  • GatherVcfs.runtime_attr_override (RuntimeAttr?)
  • GenomicsDbImport.runtime_attr_override (RuntimeAttr?)
  • GenotypeGVCFs.input_gvcf_index (File?)
  • GenotypeGVCFs.runtime_attr_override (RuntimeAttr?)
  • MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • MergeMultiAllelicSitesPostRecalibration.runtime_attr_override (RuntimeAttr?)
  • NormalizeVcfSplittingMultiallelics.runtime_attr_override (RuntimeAttr?)
  • SplitContigToIntervals.runtime_attr_override (RuntimeAttr?)
  • VariantRecalibratorIndel.runtime_attr_override (RuntimeAttr?)
  • VariantRecalibratorSnp.runtime_attr_override (RuntimeAttr?)

Defaults

  • CreateSampleNameMap.background_sample_gvcfs (Array[File], default=[])
  • GenomicsDbImport.batch_size (Int, default=100)
  • GenotypeGVCFs.batch_size (Int, default=100)
  • MakeChrIntervalList.filter (Array[String], default=['random', 'chrUn', 'decoy', 'alt', 'HLA', 'EBV'])
  • NormalizeVcfSplittingMultiallelics.batch_size (Int, default=100)
  • SplitContigToIntervals.size (Int, default=200000)

Outputs

  • joint_recalibrated_vcf (File)
  • joint_recalibrated_vcf_tbi (File)

Dot Diagram

SRJointCallGVCFsWithGenomicsDB_Pf_Niare_VQSR