PBCCSWholeGenome

PBCCSWholeGenome

description
A workflow that performs single sample variant calling on PacBio HiFi reads from one or more flow cells. The workflow merges multiple SMRT cells into a single BAM prior to variant calling.

Inputs

Required

  • aligned_bais (Array[File], required): GCS path to aligned BAM file indices
  • aligned_bams (Array[File], required): GCS path to aligned BAM files
  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • participant_name (String, required): name of the participant from whom these samples were obtained
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations

Optional

  • bed_to_compute_coverage (File?)
  • call_small_vars_on_mitochondria (Boolean?): if false, will not attempt to call variants on mitochondria; if true, some samples might fail (caller feature) due to lack of signal
  • dvp_memory (Int?)
  • dvp_threads (Int?)
  • fast_less_sensitive_sv (Boolean?): to trade less sensitive SV calling for faster speed
  • ref_scatter_interval_list_ids (File?): A file that gives short IDs to the interval_list files; needed only when running DV-Pepper
  • ref_scatter_interval_list_locator (File?): A file holding paths to interval_list files; needed only when running DV-Pepper
  • run_dv_pepper_analysis (Boolean?): to turn on DV-Pepper analysis or not (non-trivial increase in cost and runtime)
  • sites_vcf (File?): for use with Clair
  • sites_vcf_tbi (File?): for use with Clair
  • FinalizeBai.keyfile (File?)
  • FinalizeBai.runtime_attr_override (RuntimeAttr?)
  • FinalizeBam.keyfile (File?)
  • FinalizeBam.runtime_attr_override (RuntimeAttr?)
  • FinalizeClairGTbi.keyfile (File?)
  • FinalizeClairGTbi.name (String?)
  • FinalizeClairGTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeClairGVcf.keyfile (File?)
  • FinalizeClairGVcf.name (String?)
  • FinalizeClairGVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeClairTbi.keyfile (File?)
  • FinalizeClairTbi.name (String?)
  • FinalizeClairTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeClairVcf.keyfile (File?)
  • FinalizeClairVcf.name (String?)
  • FinalizeClairVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeDVPEPPERPhasedTbi.keyfile (File?)
  • FinalizeDVPEPPERPhasedTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeDVPEPPERPhasedVcf.keyfile (File?)
  • FinalizeDVPEPPERPhasedVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeDVPepperGTbi.keyfile (File?)
  • FinalizeDVPepperGTbi.name (String?)
  • FinalizeDVPepperGTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeDVPepperGVcf.keyfile (File?)
  • FinalizeDVPepperGVcf.name (String?)
  • FinalizeDVPepperGVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizeDVPepperTbi.keyfile (File?)
  • FinalizeDVPepperTbi.name (String?)
  • FinalizeDVPepperTbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeDVPepperVcf.keyfile (File?)
  • FinalizeDVPepperVcf.name (String?)
  • FinalizeDVPepperVcf.runtime_attr_override (RuntimeAttr?)
  • FinalizePBSV.keyfile (File?)
  • FinalizePBSV.name (String?)
  • FinalizePBSV.runtime_attr_override (RuntimeAttr?)
  • FinalizePBSVtbi.keyfile (File?)
  • FinalizePBSVtbi.name (String?)
  • FinalizePBSVtbi.runtime_attr_override (RuntimeAttr?)
  • FinalizePbi.keyfile (File?)
  • FinalizePbi.runtime_attr_override (RuntimeAttr?)
  • FinalizeRegionalCoverage.keyfile (File?)
  • FinalizeRegionalCoverage.name (String?)
  • FinalizeRegionalCoverage.runtime_attr_override (RuntimeAttr?)
  • FinalizeSniffles.keyfile (File?)
  • FinalizeSniffles.name (String?)
  • FinalizeSniffles.runtime_attr_override (RuntimeAttr?)
  • FinalizeSnifflesTbi.keyfile (File?)
  • FinalizeSnifflesTbi.name (String?)
  • FinalizeSnifflesTbi.runtime_attr_override (RuntimeAttr?)
  • IndexCCSUnalignedReads.runtime_attr_override (RuntimeAttr?)
  • MergeAllReads.runtime_attr_override (RuntimeAttr?)
  • CallVariants.Clair.chr (String?)
  • CallVariants.Clair.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MakeChrIntervalList.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MarginPhase.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MergeAndSortClairVCFs.header_definitions_file (File?)
  • CallVariants.MergeAndSortClairVCFs.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MergeAndSortClair_gVCFs.header_definitions_file (File?)
  • CallVariants.MergeAndSortClair_gVCFs.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MergeBams.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MergeDeepVariantGVCFs.header_definitions_file (File?)
  • CallVariants.MergeDeepVariantGVCFs.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MergeDeepVariantVCFs.header_definitions_file (File?)
  • CallVariants.MergeDeepVariantVCFs.runtime_attr_override (RuntimeAttr?)
  • CallVariants.MergePBSVVCFs.runtime_attr_override (RuntimeAttr?)
  • CallVariants.SmallVariantsScatter.runtime_attr_override (RuntimeAttr?)
  • CallVariants.SmallVariantsScatterPrepp.runtime_attr_override (RuntimeAttr?)
  • CallVariants.Sniffles2SV.runtime_attr_override (RuntimeAttr?)
  • CallVariants.SubsetBam.runtime_attr_override (RuntimeAttr?)
  • CallVariants.ZipAndIndexPBSV.runtime_attr_override (RuntimeAttr?)
  • CallVariants.ZipAndIndexSnifflesVCF.runtime_attr_override (RuntimeAttr?)
  • CallVariants.size_balanced_scatter.runtime_attr_override (RuntimeAttr?)
  • coverage.ComputeGenomeLength.runtime_attr_override (RuntimeAttr?)
  • coverage.MosDepthOverBed.runtime_attr_override (RuntimeAttr?)
  • coverage.NanoPlotFromBam.runtime_attr_override (RuntimeAttr?)
  • coverage.cov_over_region.runtime_attr_override (RuntimeAttr?)
  • CallVariants.CCSPepper.deep_variant.runtime_attr_override (RuntimeAttr?)
  • CallVariants.CCSPepper.get_hap_tagged_bam.runtime_attr_override (RuntimeAttr?)
  • CallVariants.PBSVslow.Call.runtime_attr_override (RuntimeAttr?)
  • CallVariants.PBSVslow.Discover.chr (String?)
  • CallVariants.PBSVslow.Discover.runtime_attr_override (RuntimeAttr?)
  • CallVariants.RunPBSV.Call.runtime_attr_override (RuntimeAttr?)
  • CallVariants.RunPBSV.Discover.chr (String?)
  • CallVariants.RunPBSV.Discover.runtime_attr_override (RuntimeAttr?)

Defaults

  • call_small_variants (Boolean, default=true): whether to call small variants
  • call_svs (Boolean, default=true): whether to call SVs
  • CallVariants.minsvlen (Int, default=50)
  • CallVariants.SmallVariantsScatter.prefix (String, default="subset")
  • CallVariants.SubsetBam.prefix (String, default="subset")
  • CallVariants.arbitrary.region (String, default="us-central1")

Outputs

  • aligned_bam (File)
  • aligned_bai (File)
  • aligned_pbi (File)
  • aligned_num_reads (Float)
  • aligned_num_bases (Float)
  • aligned_frac_bases (Float)
  • aligned_est_fold_cov (Float)
  • aligned_read_length_mean (Float)
  • aligned_read_length_median (Float)
  • aligned_read_length_stdev (Float)
  • aligned_read_length_N50 (Float)
  • average_identity (Float)
  • median_identity (Float)
  • bed_cov_summary (File?)
  • pbsv_vcf (File?)
  • pbsv_tbi (File?)
  • sniffles_vcf (File?)
  • sniffles_tbi (File?)
  • clair_vcf (File?)
  • clair_tbi (File?)
  • clair_gvcf (File?)
  • clair_gtbi (File?)
  • dvp_vcf (File?)
  • dvp_tbi (File?)
  • dvp_g_vcf (File?)
  • dvp_g_tbi (File?)
  • dvp_phased_vcf (File?)
  • dvp_phased_tbi (File?)

Dot Diagram

PBCCSWholeGenome