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

• 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