GLNexus

JointCall

description
This pipeline joint-calls GVCFs with GLNexus (https://github.com/dnanexus-rnd/GLnexus). It also permits intervals to be specified so that joint calling only takes place on a subset of intervals (this can be useful for finding duplicate samples).

Inputs

Required

  • dict (File, required): reference sequence dictionary
  • gvcfs (Array[File], required): gVCF files to perform joint calling upon
  • tbis (Array[File], required): gVCF index 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.
  • bed (File?): intervals to which joint calling should be restricted
  • config_file (File?)
  • num_cpus (Int?): number of CPUs to use
  • runtime_attr_override (RuntimeAttr?): override default runtime attributes
  • Call.runtime_attr_override (RuntimeAttr?): override default runtime attributes
  • ConcatBCFs.runtime_attr_override (RuntimeAttr?): override default runtime attributes
  • GetRanges.runtime_attr_override (RuntimeAttr?): override default runtime attributes
  • ShardVCFByRanges.runtime_attr_override (RuntimeAttr?): override default runtime attributes

Defaults

  • config (String, default="DeepVariantWGS"): configuration preset name or .yml filename
  • force_add_missing_dp (Boolean, default=false): force adding missing DP field to gVCFs
  • max_cpus (Int, default=64): maximum number of CPUs to allow
  • more_PL (Boolean, default=false): include PL from reference bands and other cases omitted by default
  • prefix (String, default="out"): output prefix for joined-called BCF and GVCF files
  • squeeze (Boolean, default=false): reduce pVCF size by suppressing detail in cells derived from reference bands
  • trim_uncalled_alleles (Boolean, default=false): remove alleles with no output GT calls in postprocessing
  • ConcatBCFs.is_gvcf (Boolean, default=false)
  • ConcatBCFs.num_cpus (Int, default=4): number of CPUs to use

Outputs

  • joint_vcf (File)
  • joint_vcf_tbi (File)

Dot Diagram

GLNexus