VcfLib: Vcf ROC generator¶

vcfroc · 1 contributor · 1 version

usage: vcfroc [options] [<vcf file>]

options:

`-t, --truth-vcf FILE`
	use this VCF as ground truth for ROC generation
`-w, --window-size N`
	compare records up to this many bp away (default 30)
`-r, --reference FILE`
	FASTA reference file

Quickstart¶

from janis_bioinformatics.tools.vcflib.vcfroc.versions import VcfRoc_1_0_1

wf = WorkflowBuilder("myworkflow")

wf.step(
    "vcfroc_step",
    VcfRoc_1_0_1(
        vcf=None,
        truth=None,
        reference=None,
    )
)
wf.output("out", source=vcfroc_step.out)

OR

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

Note

More information about these inputs are available below.

Generate user input files for vcfroc:

# user inputs
janis inputs vcfroc > inputs.yaml

inputs.yaml

reference: reference.fasta
truth: truth.vcf.gz
vcf: vcf.vcf.gz

Run vcfroc with:

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

Information¶

ID:	`vcfroc`
URL:	https://github.com/vcflib/vcflib
Versions:	v1.0.1
Container:	shollizeck/vcflib:1.0.1
Authors:	Sebastian Hollizeck
Citations:	None
Created:	2019-10-18
Updated:	2019-10-18

Outputs¶

name	type	documentation
out	stdout<VCF>	VCF output

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Gzipped<VCF>		3
truth	Gzipped<VCF>	-t		use this VCF as ground truth for ROC generation
reference	FastaWithIndexes	-r		FASTA reference file
windowSize	Optional<Integer>	-w		compare records up to this many bp away (default 30)

Workflow Description Language¶

version development

task vcfroc {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
    File truth
    Int? windowSize
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
  }
  command <<<
    set -e
    vcfroc \
      -t '~{truth}' \
      ~{if defined(select_first([windowSize, 30])) then ("-w " + select_first([windowSize, 30])) else ''} \
      -r '~{reference}' \
      '~{vcf}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "shollizeck/vcflib:1.0.1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    File out = stdout()
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'VcfLib: Vcf ROC generator'
doc: |-
  usage: vcfroc [options] [<vcf file>]

  options:
     -t, --truth-vcf FILE    use this VCF as ground truth for ROC generation
     -w, --window-size N       compare records up to this many bp away (default 30)
     -r, --reference FILE    FASTA reference file

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: shollizeck/vcflib:1.0.1

inputs:
- id: vcf
  label: vcf
  type: File
  inputBinding:
    position: 3
- id: truth
  label: truth
  doc: use this VCF as ground truth for ROC generation
  type: File
  inputBinding:
    prefix: -t
- id: windowSize
  label: windowSize
  doc: compare records up to this many bp away (default 30)
  type: int
  default: 30
  inputBinding:
    prefix: -w
- id: reference
  label: reference
  doc: FASTA reference file
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
  inputBinding:
    prefix: -r

outputs:
- id: out
  label: out
  doc: VCF output
  type: stdout
stdout: _stdout
stderr: _stderr

baseCommand: vcfroc
arguments: []

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