Combine Variants

combinevariants · 2 contributors · 1 version

usage: combine_vcf.py [-h] -i I –columns COLUMNS -o O –type

{germline,somatic} [–regions REGIONS] [–normal NORMAL] [–tumor TUMOR] [–priority PRIORITY [PRIORITY …]]

Extracts and combines the information from germline / somatic vcfs into one

required arguments:

-i I	input vcfs, the priority of the vcfs will be based on the order of the input. This parameter can be specified more than once
--columns COLUMNS
	Columns to keep. This parameter can be specified more than once
-o O	output vcf (unsorted)

–type {germline,somatic}

must be either germline or somatic

--regions REGIONS
	Region file containing all the variants, used as samtools mpileup
--normal NORMAL
	Sample id of germline vcf, or normal sample id of somatic vcf
--tumor TUMOR	tumor sample ID, required if inputs are somatic vcfs

–priority PRIORITY [PRIORITY …]

The priority of the callers, must match with the callers in the source header

optional arguments:

-h, --help

show this help message and exit

Quickstart

from janis_bioinformatics.tools.pmac.combinevariants.versions import CombineVariants_0_0_8

wf = WorkflowBuilder("myworkflow")

wf.step(
    "combinevariants_step",
    CombineVariants_0_0_8(
        vcfs=None,
        type=None,
    )
)
wf.output("out", source=combinevariants_step.out)

OR

1. Install Janis
2. Ensure Janis is configured to work with Docker or Singularity.
3. Ensure all reference files are available:

Note

More information about these inputs are available below.

4. Generate user input files for combinevariants:

# user inputs
janis inputs combinevariants > inputs.yaml

inputs.yaml

type: <value>
vcfs:
- vcfs_0.vcf
- vcfs_1.vcf

5. Run combinevariants with:

janis run [...run options] \
    --inputs inputs.yaml \
    combinevariants

Information

ID:combinevariants URL:https://github.com/PMCC-BioinformaticsCore/scripts/tree/master/vcf_utils Versions:0.0.8 Container:michaelfranklin/pmacutil:0.0.8 Authors:Jiaan Yu, Michael Franklin Citations:None Created:2019-03-25 00:00:00 Updated:2019-07-04 00:00:00

Outputs

name	type	documentation
out	VCF

Additional configuration (inputs)

name	type	prefix	position	documentation
vcfs	Array<VCF>	-i		input vcfs, the priority of the vcfs will be based on the order of the input
type	String	–type		germline | somatic
outputFilename	Optional<Filename>	-o
columns	Optional<Array<String>>	–columns		Columns to keep, seperated by space output vcf (unsorted)
normal	Optional<String>	–normal		Sample id of germline vcf, or normal sample id of somatic vcf
tumor	Optional<String>	–tumor		tumor sample ID, required if inputs are somatic vcfs
priority	Optional<Integer>	–priority		The priority of the callers, must match with the callers in the source header

Workflow Description Language

version development

task combinevariants {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    String? outputFilename
    Array[File] vcfs
    String type
    Array[String]? columns
    String? normal
    String? tumor
    Int? priority
  }
  command <<<
    set -e
    combine_vcf.py \
      -o '~{select_first([outputFilename, "generated.combined.vcf"])}' \
      ~{if length(vcfs) > 0 then "-i '" + sep("' -i '", vcfs) + "'" else ""} \
      --type '~{type}' \
      ~{if (defined(columns) && length(select_first([columns])) > 0) then "--columns '" + sep("','", select_first([columns])) + "'" else ""} \
      ~{if defined(normal) then ("--normal '" + normal + "'") else ""} \
      ~{if defined(tumor) then ("--tumor '" + tumor + "'") else ""} \
      ~{if defined(priority) then ("--priority " + priority) else ''}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "michaelfranklin/pmacutil:0.0.8"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.combined.vcf"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Combine Variants
doc: |2

  usage: combine_vcf.py [-h] -i I --columns COLUMNS -o O --type
                        {germline,somatic} [--regions REGIONS] [--normal NORMAL]
                        [--tumor TUMOR] [--priority PRIORITY [PRIORITY ...]]

  Extracts and combines the information from germline / somatic vcfs into one

  required arguments:
    -i I                  input vcfs, the priority of the vcfs will be based on
                          the order of the input. This parameter can be
                          specified more than once
    --columns COLUMNS     Columns to keep. This parameter can be specified more
                          than once
    -o O                  output vcf (unsorted)
    --type {germline,somatic}
                          must be either germline or somatic
    --regions REGIONS     Region file containing all the variants, used as
                          samtools mpileup
    --normal NORMAL       Sample id of germline vcf, or normal sample id of
                          somatic vcf
    --tumor TUMOR         tumor sample ID, required if inputs are somatic vcfs
    --priority PRIORITY [PRIORITY ...]
                          The priority of the callers, must match with the
                          callers in the source header

  optional arguments:
    -h, --help            show this help message and exit

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: michaelfranklin/pmacutil:0.0.8

inputs:
- id: outputFilename
  label: outputFilename
  type:
  - string
  - 'null'
  default: generated.combined.vcf
  inputBinding:
    prefix: -o
- id: vcfs
  label: vcfs
  doc: input vcfs, the priority of the vcfs will be based on the order of the input
  type:
    type: array
    inputBinding:
      prefix: -i
    items: File
  inputBinding: {}
- id: type
  label: type
  doc: germline | somatic
  type: string
  inputBinding:
    prefix: --type
- id: columns
  label: columns
  doc: Columns to keep, seperated by space output vcf (unsorted)
  type:
  - type: array
    items: string
  - 'null'
  inputBinding:
    prefix: --columns
    itemSeparator: ','
- id: normal
  label: normal
  doc: Sample id of germline vcf, or normal sample id of somatic vcf
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --normal
- id: tumor
  label: tumor
  doc: tumor sample ID, required if inputs are somatic vcfs
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --tumor
- id: priority
  label: priority
  doc: The priority of the callers, must match with the callers in the source header
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --priority

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.combined.vcf
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: combine_vcf.py
arguments: []

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: combinevariants