VcfTools: VcfConcat¶

VcfToolsVcfConcat · 1 contributor · 1 version

Concatenates VCF files (for example split by chromosome). Note that the input and output VCFs will have the same number of columns, the script does not merge VCFs by position (see also vcf-merge).

In the basic mode it does not do anything fancy except for a sanity check that all files have the same columns. When run with the -s option, it will perform a partial merge sort, looking at limited number of open files simultaneously.

Quickstart¶

from janis_bioinformatics.tools.vcftools.vcfconcat.versions import VcfToolsVcfConcat_0_1_16

wf = WorkflowBuilder("myworkflow")

wf.step(
    "vcftoolsvcfconcat_step",
    VcfToolsVcfConcat_0_1_16(
        vcfTabix=None,
    )
)
wf.output("out", source=vcftoolsvcfconcat_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 VcfToolsVcfConcat:

# user inputs
janis inputs VcfToolsVcfConcat > inputs.yaml

inputs.yaml

vcfTabix:
- vcfTabix_0.vcf.gz
- vcfTabix_1.vcf.gz

Run VcfToolsVcfConcat with:

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

Information¶

ID:	`VcfToolsVcfConcat`
URL:	http://vcftools.sourceforge.net/perl_module.html#vcf-concat
Versions:	0.1.16
Container:	biocontainers/vcftools:v0.1.16-1-deb_cv1
Authors:	Jiaan Yu
Citations:	None
Created:	2020-05-21
Updated:	2020-05-21

Outputs¶

name	type	documentation
out	stdout<VCF>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcfTabix	Array<Gzipped<VCF>>		10
checkColumns	Optional<Boolean>	-c		Do not concatenate, only check if the columns agree.
padMissing	Optional<Boolean>	-p		Write ‘.’ in place of missing columns. Useful for joining chrY with the rest.
mergeSort	Optional<Integer>	–merge-sort		Allow small overlaps in N consecutive files.

Workflow Description Language¶

version development

task VcfToolsVcfConcat {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Boolean? checkColumns
    Boolean? padMissing
    Int? mergeSort
    Array[File] vcfTabix
    Array[File] vcfTabix_tbi
  }
  command <<<
    set -e
     vcf-concat \
      ~{if (defined(checkColumns) && select_first([checkColumns])) then "-c" else ""} \
      ~{if (defined(padMissing) && select_first([padMissing])) then "-p" else ""} \
      ~{if defined(mergeSort) then ("--merge-sort " + mergeSort) else ''} \
      ~{if length(vcfTabix) > 0 then "'" + sep("' '", vcfTabix) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "biocontainers/vcftools:v0.1.16-1-deb_cv1"
    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: 'VcfTools: VcfConcat'
doc: |-
  Concatenates VCF files (for example split by chromosome). Note that the input and output VCFs will have the same number of columns, the script does not merge VCFs by position (see also vcf-merge).

  In the basic mode it does not do anything fancy except for a sanity check that all files have the same columns. When run with the -s option, it will perform a partial merge sort, looking at limited number of open files simultaneously.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: biocontainers/vcftools:v0.1.16-1-deb_cv1

inputs:
- id: checkColumns
  label: checkColumns
  doc: Do not concatenate, only check if the columns agree.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -c
- id: padMissing
  label: padMissing
  doc: Write '.' in place of missing columns. Useful for joining chrY with the rest.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -p
- id: mergeSort
  label: mergeSort
  doc: Allow small overlaps in N consecutive files.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --merge-sort
- id: vcfTabix
  label: vcfTabix
  type:
    type: array
    items: File
  inputBinding:
    position: 10

outputs:
- id: out
  label: out
  type: stdout
stdout: _stdout
stderr: _stderr

baseCommand:
- ''
- vcf-concat
arguments: []

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