BCFTools: View

bcftoolsview · 1 contributor · 2 versions

---

View, subset and filter VCF or BCF files by position and filtering expression Convert between VCF and BCF. Former bcftools subset.

Quickstart

from janis_bioinformatics.tools.bcftools.view.versions import BcfToolsView_1_9

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bcftoolsview_step",
    BcfToolsView_1_9(
        file=None,
    )
)
wf.output("out", source=bcftoolsview_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 bcftoolsview:

# user inputs
janis inputs bcftoolsview > inputs.yaml

inputs.yaml

file: file.vcf.gz

5. Run bcftoolsview with:

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

Information

ID:bcftoolsview URL:https://samtools.github.io/bcftools/bcftools.html#view Versions:v1.9, v1.5 Container:biocontainers/bcftools:v1.9-1-deb_cv1 Authors:Michael Franklin Citations:Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, and 1000 Genome Project Data Processing Subgroup, The Sequence alignment/map (SAM) format and SAMtools, Bioinformatics (2009) 25(16) 2078-9 DOI:http://www.ncbi.nlm.nih.gov/pubmed/19505943 Created:2019-01-24 Updated:2019-01-24

Outputs

name	type	documentation
out	stdout<Gzipped<VCF>>

Additional configuration (inputs)

name	type	prefix	position	documentation
file	Gzipped<VCF>		2
dropGenotypes	Optional<Boolean>	–drop-genotypes	1	(-G) drop individual genotype information (after subsetting if -s option set)
headerOnly	Optional<Boolean>	–header-only	1	(-h) print the header only
noHeader	Optional<Boolean>	–no-header	1	(-H) suppress the header in VCF output
compressionLevel	Optional<Integer>	–compression-level	1	(-l) compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]
noVersion	Optional<Boolean>	–no-version	1	do not append version and command line to the header
regions	Optional<String>	–regions	1	(-r) restrict to comma-separated list of regions
regionsFile	Optional<File>	–regions-file	1	(-R) restrict to regions listed in a file
targets	Optional<String>	–targets	1	(-t) similar to -r but streams rather than index-jumps. Exclude regions with ‘^’ prefix
targetsFile	Optional<File>	–targets-file	1	(-T) similar to -R but streams rather than index-jumps. Exclude regions with ‘^’ prefix
threads	Optional<Integer>	–threads	1	number of extra output compression threads [0]
trimAltAlleles	Optional<Boolean>	–trim-alt-alleles	1	(-a) trim alternate alleles not seen in the subset
noUpdate	Optional<Boolean>	–no-update	1	(-I) do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
samples	Optional<Array<String>>	–samples	1	(-s) comma separated list of samples to include (or exclude with ‘^’ prefix)
samplesFile	Optional<File>	–samples-file	1	(-S) file of samples to include (or exclude with ‘^’ prefix)
forceSamples	Optional<Boolean>	–force-samples	1	only warn about unknown subset samples
minAc	Optional<Integer>	–min-ac	1	(-c) minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
maxAc	Optional<Integer>	–max-ac	1	(-C) maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
applyFilters	Optional<Array<String>>	–apply-filters	1	(-f) require at least one of the listed FILTER strings (e.g. ‘PASS,.’’)
genotype	Optional<String>	–genotype	1	(-g) [<hom|het|miss>] require one or more hom/het/missing genotype or, if prefixed with ‘^’, exclude sites with hom/het/missing genotypes
include	Optional<String>	–include	1	(-i) select sites for which the expression is true (see man page for details)
exclude	Optional<String>	–exclude	1	(-e) exclude sites for which the expression is true (see man page for details)
known	Optional<Boolean>	–known	1	(-k) select known sites only (ID is not/is ‘.’)
novel	Optional<Boolean>	–novel	1	(-n) select novel sites only (ID is not/is ‘.’)
minAlleles	Optional<Integer>	–min-alleles	1	(-m) minimum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
maxAlleles	Optional<Integer>	–max-alleles	1	(-M) maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
phased	Optional<Boolean>	–phased	1	(-p) select sites where all samples are phased
excludePhased	Optional<Boolean>	–exclude-phased	1	(-P) exclude sites where all samples are phased
minAf	Optional<Float>	–min-af	1	(-q) minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
maxAf	Optional<Float>	–max-af	1	(-Q) maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
uncalled	Optional<Boolean>	–uncalled	1	(-u) select sites without a called genotype
excludeUncalled	Optional<Boolean>	–exclude-uncalled	1	(-U) exclude sites without a called genotype
types	Optional<Array<String>>	–types	1	(-v) select comma-separated list of variant types: snps,indels,mnps,other [null]
excludeTypes	Optional<Array<String>>	–exclude-types	1	(-V) exclude comma-separated list of variant types: snps,indels,mnps,other [null]
private	Optional<Boolean>	–private	1	(-x) select sites where the non-reference alleles are exclusive (private) to the subset samples
excludePrivate	Optional<Boolean>	–exclude-private	1	(-X) exclude sites where the non-reference alleles are exclusive (private) to the subset samples

Workflow Description Language

version development

task bcftoolsview {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File file
    Boolean? dropGenotypes
    Boolean? headerOnly
    Boolean? noHeader
    Int? compressionLevel
    Boolean? noVersion
    String? regions
    File? regionsFile
    String? targets
    File? targetsFile
    Int? threads
    Boolean? trimAltAlleles
    Boolean? noUpdate
    Array[String]? samples
    File? samplesFile
    Boolean? forceSamples
    Int? minAc
    Int? maxAc
    Array[String]? applyFilters
    String? genotype
    String? include
    String? exclude
    Boolean? known
    Boolean? novel
    Int? minAlleles
    Int? maxAlleles
    Boolean? phased
    Boolean? excludePhased
    Float? minAf
    Float? maxAf
    Boolean? uncalled
    Boolean? excludeUncalled
    Array[String]? types
    Array[String]? excludeTypes
    Boolean? private
    Boolean? excludePrivate
  }
  command <<<
    set -e
    bcftools view \
      ~{if (defined(dropGenotypes) && select_first([dropGenotypes])) then "--drop-genotypes" else ""} \
      ~{if (defined(headerOnly) && select_first([headerOnly])) then "--header-only" else ""} \
      ~{if (defined(noHeader) && select_first([noHeader])) then "--no-header" else ""} \
      ~{if defined(compressionLevel) then ("--compression-level " + compressionLevel) else ''} \
      ~{if (defined(noVersion) && select_first([noVersion])) then "--no-version" else ""} \
      ~{if defined(regions) then ("--regions '" + regions + "'") else ""} \
      ~{if defined(regionsFile) then ("--regions-file '" + regionsFile + "'") else ""} \
      ~{if defined(targets) then ("--targets '" + targets + "'") else ""} \
      ~{if defined(targetsFile) then ("--targets-file '" + targetsFile + "'") else ""} \
      ~{if defined(threads) then ("--threads " + threads) else ''} \
      ~{if (defined(trimAltAlleles) && select_first([trimAltAlleles])) then "--trim-alt-alleles" else ""} \
      ~{if (defined(noUpdate) && select_first([noUpdate])) then "--no-update" else ""} \
      ~{if (defined(samples) && length(select_first([samples])) > 0) then "--samples '" + sep("' '", select_first([samples])) + "'" else ""} \
      ~{if defined(samplesFile) then ("--samples-file '" + samplesFile + "'") else ""} \
      ~{if (defined(forceSamples) && select_first([forceSamples])) then "--force-samples" else ""} \
      ~{if defined(minAc) then ("--min-ac " + minAc) else ''} \
      ~{if defined(maxAc) then ("--max-ac " + maxAc) else ''} \
      ~{if (defined(applyFilters) && length(select_first([applyFilters])) > 0) then "--apply-filters '" + sep("' '", select_first([applyFilters])) + "'" else ""} \
      ~{if defined(genotype) then ("--genotype '" + genotype + "'") else ""} \
      ~{if defined(include) then ("--include '" + include + "'") else ""} \
      ~{if defined(exclude) then ("--exclude '" + exclude + "'") else ""} \
      ~{if (defined(known) && select_first([known])) then "--known" else ""} \
      ~{if (defined(novel) && select_first([novel])) then "--novel" else ""} \
      ~{if defined(minAlleles) then ("--min-alleles " + minAlleles) else ''} \
      ~{if defined(maxAlleles) then ("--max-alleles " + maxAlleles) else ''} \
      ~{if (defined(phased) && select_first([phased])) then "--phased" else ""} \
      ~{if (defined(excludePhased) && select_first([excludePhased])) then "--exclude-phased" else ""} \
      ~{if defined(minAf) then ("--min-af " + minAf) else ''} \
      ~{if defined(maxAf) then ("--max-af " + maxAf) else ''} \
      ~{if (defined(uncalled) && select_first([uncalled])) then "--uncalled" else ""} \
      ~{if (defined(excludeUncalled) && select_first([excludeUncalled])) then "--exclude-uncalled" else ""} \
      ~{if (defined(types) && length(select_first([types])) > 0) then "--types '" + sep("' '", select_first([types])) + "'" else ""} \
      ~{if (defined(excludeTypes) && length(select_first([excludeTypes])) > 0) then "--exclude-types '" + sep("' '", select_first([excludeTypes])) + "'" else ""} \
      ~{if (defined(private) && select_first([private])) then "--private" else ""} \
      ~{if (defined(excludePrivate) && select_first([excludePrivate])) then "--exclude-private" else ""} \
      --output-type 'z' \
      '~{file}'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "biocontainers/bcftools:v1.9-1-deb_cv1"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 8, 4])}G"
    preemptible: 2
  }
  output {
    File out = stdout()
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'BCFTools: View'
doc: |-
  ________________________________

          View, subset and filter VCF or BCF files by position and filtering expression
          Convert between VCF and BCF. Former bcftools subset.

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: biocontainers/bcftools:v1.9-1-deb_cv1

inputs:
- id: file
  label: file
  type: File
  inputBinding:
    position: 2
- id: dropGenotypes
  label: dropGenotypes
  doc: (-G) drop individual genotype information (after subsetting if -s option set)
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --drop-genotypes
    position: 1
- id: headerOnly
  label: headerOnly
  doc: (-h) print the header only
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --header-only
    position: 1
- id: noHeader
  label: noHeader
  doc: (-H) suppress the header in VCF output
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-header
    position: 1
- id: compressionLevel
  label: compressionLevel
  doc: '(-l) compression level: 0 uncompressed, 1 best speed, 9 best compression [-1]'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --compression-level
    position: 1
- id: noVersion
  label: noVersion
  doc: do not append version and command line to the header
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-version
    position: 1
- id: regions
  label: regions
  doc: (-r) restrict to comma-separated list of regions
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --regions
    position: 1
- id: regionsFile
  label: regionsFile
  doc: (-R) restrict to regions listed in a file
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --regions-file
    position: 1
- id: targets
  label: targets
  doc: |-
    (-t) similar to -r but streams rather than index-jumps. Exclude regions with '^' prefix
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --targets
    position: 1
- id: targetsFile
  label: targetsFile
  doc: |-
    (-T) similar to -R but streams rather than index-jumps. Exclude regions with '^' prefix
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --targets-file
    position: 1
- id: threads
  label: threads
  doc: number of extra output compression threads [0]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --threads
    position: 1
- id: trimAltAlleles
  label: trimAltAlleles
  doc: (-a) trim alternate alleles not seen in the subset
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --trim-alt-alleles
    position: 1
- id: noUpdate
  label: noUpdate
  doc: |-
    (-I) do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-update
    position: 1
- id: samples
  label: samples
  doc: (-s) comma separated list of samples to include (or exclude with '^' prefix)
  type:
  - type: array
    items: string
  - 'null'
  inputBinding:
    prefix: --samples
    position: 1
- id: samplesFile
  label: samplesFile
  doc: (-S) file of samples to include (or exclude with '^' prefix)
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --samples-file
    position: 1
- id: forceSamples
  label: forceSamples
  doc: only warn about unknown subset samples
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --force-samples
    position: 1
- id: minAc
  label: minAc
  doc: |-
    (-c) minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-ac
    position: 1
- id: maxAc
  label: maxAc
  doc: |-
    (-C) maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --max-ac
    position: 1
- id: applyFilters
  label: applyFilters
  doc: (-f) require at least one of the listed FILTER strings (e.g. 'PASS,.'')
  type:
  - type: array
    items: string
  - 'null'
  inputBinding:
    prefix: --apply-filters
    position: 1
- id: genotype
  label: genotype
  doc: |-
    (-g) [<hom|het|miss>] require one or more hom/het/missing genotype or, if prefixed with '^', exclude sites with hom/het/missing genotypes
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --genotype
    position: 1
- id: include
  label: include
  doc: (-i) select sites for which the expression is true (see man page for details)
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --include
    position: 1
- id: exclude
  label: exclude
  doc: (-e) exclude sites for which the expression is true (see man page for details)
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --exclude
    position: 1
- id: known
  label: known
  doc: (-k) select known sites only (ID is not/is '.')
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --known
    position: 1
- id: novel
  label: novel
  doc: (-n) select novel sites only (ID is not/is '.')
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --novel
    position: 1
- id: minAlleles
  label: minAlleles
  doc: |-
    (-m) minimum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --min-alleles
    position: 1
- id: maxAlleles
  label: maxAlleles
  doc: |-
    (-M) maximum number of alleles listed in REF and ALT (e.g. -m2 -M2 for biallelic sites)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --max-alleles
    position: 1
- id: phased
  label: phased
  doc: (-p) select sites where all samples are phased
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --phased
    position: 1
- id: excludePhased
  label: excludePhased
  doc: (-P) exclude sites where all samples are phased
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --exclude-phased
    position: 1
- id: minAf
  label: minAf
  doc: |-
    (-q) minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
  type:
  - float
  - 'null'
  inputBinding:
    prefix: --min-af
    position: 1
- id: maxAf
  label: maxAf
  doc: |-
    (-Q) maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles [nref]
  type:
  - float
  - 'null'
  inputBinding:
    prefix: --max-af
    position: 1
- id: uncalled
  label: uncalled
  doc: (-u) select sites without a called genotype
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --uncalled
    position: 1
- id: excludeUncalled
  label: excludeUncalled
  doc: (-U) exclude sites without a called genotype
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --exclude-uncalled
    position: 1
- id: types
  label: types
  doc: '(-v) select comma-separated list of variant types: snps,indels,mnps,other
    [null]'
  type:
  - type: array
    items: string
  - 'null'
  inputBinding:
    prefix: --types
    position: 1
- id: excludeTypes
  label: excludeTypes
  doc: |-
    (-V) exclude comma-separated list of variant types: snps,indels,mnps,other [null]
  type:
  - type: array
    items: string
  - 'null'
  inputBinding:
    prefix: --exclude-types
    position: 1
- id: private
  label: private
  doc: |-
    (-x) select sites where the non-reference alleles are exclusive (private) to the subset samples
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --private
    position: 1
- id: excludePrivate
  label: excludePrivate
  doc: |-
    (-X) exclude sites where the non-reference alleles are exclusive (private) to the subset samples
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --exclude-private
    position: 1

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

baseCommand:
- bcftools
- view
arguments:
- prefix: --output-type
  position: 1
  valueFrom: z

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