SplitMultiSampleVCF

SplitMultiSampleVCF

description
Split a multi-sample VCF into individual compressed VCF files, one per sample, with corresponding index files.
author
Jonn Smith

Inputs

Required

  • input_vcf (File, required): Multi-sample VCF file (can be compressed or uncompressed)

Optional

  • input_vcf_index (File?): Index file for the input VCF (required if VCF is compressed)
  • sample_name_list (File?): Optional file containing sample names to extract, one per line. Same semantics as sample_names. Mutually exclusive with sample_names.
  • sample_names (Array[String]?): Optional list of sample names to extract. If provided, every name must occur in input_vcf; the workflow fails (listing all absent names) when any is missing. Only the listed samples are emitted; otherwise every sample is emitted. Mutually exclusive with sample_name_list.
  • SplitMultiSampleVCFTask.runtime_attr_override (RuntimeAttr?)

Defaults

  • disk_space_multiplier (Int, default=4): Multiplier applied to the input VCF size when sizing the task's disk (optional; default: 4)

Outputs

  • sample_vcfs (Array[File])
  • sample_vcf_indices (Array[File])

Dot Diagram

SplitMultiSampleVCF