SRJointGenotyping

CreateSampleNameMap

description
Creates the sample / name-map file of the GVCFs for ingest into ImportGVCFs. NOTE: Some of this functionality is duplicated from Utils.InferSampleName. This is intentional - we don't want to localize all these files or shard over potentially thousands of input GVCFs.

Inputs

Required

  • gvcfs (Array[File], required): Array of single-sample GVCF files.; localization_optional: true
  • prefix (String, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • background_sample_gvcfs (Array[File], default=[]): Array of single-sample GVCF files to use as background samples for joint calling.; localization_optional: true

Outputs

  • sample_name_map (File)
  • total_gvcf_size_gb (Int)

ImportGVCFs

Inputs

Required

  • interval_list (File, required)
  • prefix (String, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_fai (File, required)
  • sample_name_map (File, required)

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • batch_size (Int, default=50)
  • extra_mem_gb (Int, default=0)

Outputs

  • output_genomicsdb (File)

GenotypeGVCFs

Inputs

Required

  • input_gvcf_data (File, required): Either a single GVCF file or a GenomicsDB Tar file.
  • interval_list (File, required); localization_optional: true
  • prefix (String, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_fai (File, required)

Optional

  • dbsnp_vcf (String?)
  • input_gvcf_index (File?)
  • runtime_attr_override (RuntimeAttr?)

Defaults

  • heterozygosity (Float, default=0.001)
  • heterozygosity_stdev (Float, default=0.01)
  • indel_heterozygosity (Float, default=0.000125)
  • keep_combined_raw_annotations (Boolean, default=false)

Outputs

  • output_vcf (File)
  • output_vcf_index (File)

GnarlyGenotypeGVCFs

Inputs

Required

  • input_gvcf_data (File, required): Either a single GVCF file or a GenomicsDB Tar file.
  • interval_list (File, required); localization_optional: true
  • prefix (String, required)
  • ref_dict (File, required)
  • ref_fasta (File, required)
  • ref_fasta_fai (File, required)

Optional

  • dbsnp_vcf (String?)
  • input_gvcf_index (File?)
  • runtime_attr_override (RuntimeAttr?)

Defaults

  • heterozygosity (Float, default=0.001)
  • heterozygosity_stdev (Float, default=0.01)
  • indel_heterozygosity (Float, default=0.000125)
  • keep_combined_raw_annotations (Boolean, default=false)

Outputs

  • output_vcf (File)
  • output_vcf_index (File)