LRJointCallGVCFs

LRJointCallGVCFs

description
A workflow that performs joint calling on gVCFs (usually from DeepVariant) using GLNexus.

Inputs

Required

  • gcs_out_root_dir (String, required): GCS bucket to store the reads, variants, and metrics files
  • gvcfs (Array[File], required): GCS paths to gVCF files
  • prefix (String, required): prefix for output joint-called gVCF and tabix index
  • ref_map_file (File, required): table indicating reference sequence and auxillary file locations
  • tbis (Array[File], required): GCS paths to gVCF tbi files

Optional

  • background_sample_gvcf_indices (Array[Array[File]]?): Array of GVCF index files for background_sample_gvcfs. Order should correspond to that in background_sample_gvcfs.
  • background_sample_gvcfs (Array[Array[File]]?): Array of GVCFs to use as background samples for joint calling.
  • ConvertToHailMT.ref_fai (String?)
  • ConvertToHailMT.ref_fasta (String?)
  • ConvertToHailMT.runtime_attr_override (RuntimeAttr?)
  • FinalizeMT.keyfile (File?)
  • FinalizeMT.name (String?)
  • FinalizeMT.runtime_attr_override (RuntimeAttr?)
  • FinalizeTBI.keyfile (File?)
  • FinalizeTBI.name (String?)
  • FinalizeTBI.runtime_attr_override (RuntimeAttr?)
  • FinalizeVCF.keyfile (File?)
  • FinalizeVCF.name (String?)
  • FinalizeVCF.runtime_attr_override (RuntimeAttr?)
  • JointCall.bed (File?)
  • JointCall.config_file (File?)
  • JointCall.num_cpus (Int?)
  • JointCall.runtime_attr_override (RuntimeAttr?)
  • JointCall.Call.runtime_attr_override (RuntimeAttr?)
  • JointCall.ConcatBCFs.runtime_attr_override (RuntimeAttr?)
  • JointCall.GetRanges.runtime_attr_override (RuntimeAttr?)
  • JointCall.ShardVCFByRanges.runtime_attr_override (RuntimeAttr?)

Defaults

  • force_add_missing_dp (Boolean, default=false): force adding missing DP field to gVCFs
  • ConvertToHailMT.reference (String, default="GRCh38")
  • JointCall.config (String, default="DeepVariantWGS")
  • JointCall.max_cpus (Int, default=64)
  • JointCall.more_PL (Boolean, default=false)
  • JointCall.squeeze (Boolean, default=false)
  • JointCall.trim_uncalled_alleles (Boolean, default=false)
  • JointCall.ConcatBCFs.is_gvcf (Boolean, default=false)
  • JointCall.ConcatBCFs.num_cpus (Int, default=4)

Outputs

  • joint_vcf (File)
  • joint_vcf_tbi (File)
  • joint_mt (String)

Dot Diagram

LRJointCallGVCFs