VcfLib: VcfFixUp¶

vcffixup · 1 contributor · 1 version

usage: vcffixup [file] Count the allele frequencies across alleles

present in each record in the VCF file. (Similar to vcftools –freq.)

Uses genotypes from the VCF file to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.

Quickstart¶

from janis_bioinformatics.tools.vcflib.vcffixup.versions import VcfFixUp_1_0_1

wf = WorkflowBuilder("myworkflow")

wf.step(
    "vcffixup_step",
    VcfFixUp_1_0_1(
        vcf=None,
    )
)
wf.output("out", source=vcffixup_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 vcffixup:

# user inputs
janis inputs vcffixup > inputs.yaml

inputs.yaml

vcf: vcf.vcf.gz

Run vcffixup with:

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

Information¶

ID:	`vcffixup`
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

Workflow Description Language¶

version development

task vcffixup {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File vcf
  }
  command <<<
    set -e
    vcffixup \
      '~{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: VcfFixUp'
doc: |-
  usage: vcffixup [file]
  Count the allele frequencies across alleles
   present in each record in the VCF file. (Similar to vcftools --freq.)

  Uses genotypes from the VCF file to correct AC (alternate allele count), AF (alternate allele frequency), NS (number of called), in the VCF records.

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

inputs:
- id: vcf
  label: vcf
  type: File
  inputBinding:
    position: 3

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

baseCommand: vcffixup
arguments: []

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