vcffixup.rst

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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

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 vcffixup:

# user inputs
janis inputs vcffixup > inputs.yaml

inputs.yaml

vcf: vcf.vcf.gz

5. 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