BCFTools: Concat¶

bcftoolsConcat · 1 contributor · 1 version

Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. The program can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, –allow-overlaps option is specified. With the –naive option, the files are concatenated without being recompressed, which is very fast but dangerous if the BCF headers differ.

Quickstart¶

from janis_bioinformatics.tools.bcftools.concat.versions import BcfToolsConcat_1_9

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bcftoolsconcat_step",
    BcfToolsConcat_1_9(
        vcf=None,
    )
)
wf.output("out", source=bcftoolsconcat_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 bcftoolsConcat:

# user inputs
janis inputs bcftoolsConcat > inputs.yaml

inputs.yaml

vcf:
- vcf_0.vcf.gz
- vcf_1.vcf.gz

Run bcftoolsConcat with:

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

Information¶

ID:	`bcftoolsConcat`
URL:	https://samtools.github.io/bcftools/bcftools.html#concat
Versions:	v1.9
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:	2019-09-09
Updated:	2019-09-09

Outputs¶

name	type	documentation
out	Gzipped<VCF>

Additional configuration (inputs)¶

name	type	prefix	position	documentation
vcf	Array<Gzipped<VCF>>		15
outputFilename	Optional<Filename>	-o		–output: When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
allowOverLaps	Optional<Boolean>	-a		First coordinate of the next file can precede last record of the current file.
compactPS	Optional<Boolean>	-c		Do not output PS tag at each site, only at the start of a new phase set block.
rmDups	Optional<String>	-d		Output duplicate records present in multiple files only once: <snps\|indels\|both\|all\|none>
rmDupsNone	Optional<Boolean>	-d		Alias for -d none
fileList	Optional<File>	-f		Read the list of files from a file.
ligate	Optional<Boolean>	-l		Ligate phased VCFs by matching phase at overlapping haplotypes
noVersion	Optional<Boolean>	–no-version		Do not append version and command line information to the output VCF header.
naive	Optional<Boolean>	-n		Concatenate files without recompression (dangerous, use with caution)
outputType	Optional<String>	-O		–output-type b\|u\|z\|v: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
minPG	Optional<Integer>	-q		Break phase set if phasing quality is lower than <int> [30]
regions	Optional<String>	-r		–regions chr\|chr:pos\|chr:from-to\|chr:from-[,…]: Comma-separated list of regions, see also -R, –regions-file. Note that -r cannot be used in combination with -R.
regionsFile	Optional<File>	-R		–regions-file: Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default). The columns of the tab-delimited file are: CHROM, POS, and, optionally, POS_TO, where positions are 1-based and inclusive. The columns of the tab-delimited BED file are also CHROM, POS and POS_TO (trailing columns are ignored), but coordinates are 0-based, half-open. To indicate that a file be treated as BED rather than the 1-based tab-delimited file, the file must have the ‘.bed’ or ‘.bed.gz’ suffix (case-insensitive). Uncompressed files are stored in memory, while bgzip-compressed and tabix-indexed region files are streamed. Note that sequence names must match exactly, ‘chr20’ is not the same as ‘20’. Also note that chromosome ordering in FILE will be respected, the VCF will be processed in the order in which chromosomes first appear in FILE. However, within chromosomes, the VCF will always be processed in ascending genomic coordinate order no matter what order they appear in FILE. Note that overlapping regions in FILE can result in duplicated out of order positions in the output. This option requires indexed VCF/BCF files. Note that -R cannot be used in combination with -r.
threads	Optional<Integer>	–threads		Number of output compression threads to use in addition to main thread. Only used when –output-type is b or z. Default: 0.

Workflow Description Language¶

version development

task bcftoolsConcat {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Array[File] vcf
    String? outputFilename
    Boolean? allowOverLaps
    Boolean? compactPS
    String? rmDups
    Boolean? rmDupsNone
    File? fileList
    Boolean? ligate
    Boolean? noVersion
    Boolean? naive
    String? outputType
    Int? minPG
    String? regions
    File? regionsFile
    Int? threads
  }
  command <<<
    set -e
    bcftools concat \
      -o '~{select_first([outputFilename, "generated.vcf.gz"])}' \
      ~{if (defined(allowOverLaps) && select_first([allowOverLaps])) then "-a" else ""} \
      ~{if (defined(compactPS) && select_first([compactPS])) then "-c" else ""} \
      ~{if defined(rmDups) then ("-d '" + rmDups + "'") else ""} \
      ~{if (defined(rmDupsNone) && select_first([rmDupsNone])) then "-d" else ""} \
      ~{if defined(fileList) then ("-f '" + fileList + "'") else ""} \
      ~{if (defined(ligate) && select_first([ligate])) then "-l" else ""} \
      ~{if (defined(noVersion) && select_first([noVersion])) then "--no-version" else ""} \
      ~{if (defined(naive) && select_first([naive])) then "-n" else ""} \
      ~{if defined(select_first([outputType, "z"])) then ("-O '" + select_first([outputType, "z"]) + "'") else ""} \
      ~{if defined(minPG) then ("-q " + minPG) else ''} \
      ~{if defined(regions) then ("-r '" + regions + "'") else ""} \
      ~{if defined(regionsFile) then ("-R '" + regionsFile + "'") else ""} \
      ~{if defined(threads) then ("--threads " + threads) else ''} \
      ~{if length(vcf) > 0 then "'" + sep("' '", vcf) + "'" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 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, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "generated.vcf.gz"])
  }
}

Common Workflow Language¶

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

  Concatenate or combine VCF/BCF files. All source files must have the same sample
  columns appearing in the same order. The program can be used, for example, to
  concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
  VCF into one. The input files must be sorted by chr and position. The files
  must be given in the correct order to produce sorted VCF on output unless
  the -a, --allow-overlaps option is specified. With the --naive option, the files
  are concatenated without being recompressed, which is very fast but dangerous
  if the BCF headers differ.

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

inputs:
- id: vcf
  label: vcf
  type:
    type: array
    items: File
  inputBinding:
    position: 15
- id: outputFilename
  label: outputFilename
  doc: |-
    --output: When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default.
  type:
  - string
  - 'null'
  default: generated.vcf.gz
  inputBinding:
    prefix: -o
- id: allowOverLaps
  label: allowOverLaps
  doc: First coordinate of the next file can precede last record of the current file.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -a
- id: compactPS
  label: compactPS
  doc: Do not output PS tag at each site, only at the start of a new phase set block.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -c
- id: rmDups
  label: rmDups
  doc: |-
    Output duplicate records present in multiple files only once: <snps|indels|both|all|none>
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -d
- id: rmDupsNone
  label: rmDupsNone
  doc: Alias for -d none
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -d
- id: fileList
  label: fileList
  doc: Read the list of files from a file.
  type:
  - File
  - 'null'
  inputBinding:
    prefix: -f
- id: ligate
  label: ligate
  doc: Ligate phased VCFs by matching phase at overlapping haplotypes
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -l
- id: noVersion
  label: noVersion
  doc: Do not append version and command line information to the output VCF header.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-version
- id: naive
  label: naive
  doc: Concatenate files without recompression (dangerous, use with caution)
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -n
- id: outputType
  label: outputType
  doc: |-
    --output-type b|u|z|v: Output compressed BCF (b), uncompressed BCF (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion.
  type: string
  default: z
  inputBinding:
    prefix: -O
- id: minPG
  label: minPG
  doc: Break phase set if phasing quality is lower than <int> [30]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -q
- id: regions
  label: regions
  doc: |-
    --regions chr|chr:pos|chr:from-to|chr:from-[,…]: Comma-separated list of regions, see also -R, --regions-file. Note that -r cannot be used in combination with -R.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -r
- id: regionsFile
  label: regionsFile
  doc: |-
    --regions-file: Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default). The columns of the tab-delimited file are: CHROM, POS, and, optionally, POS_TO, where positions are 1-based and inclusive. The columns of the tab-delimited BED file are also CHROM, POS and POS_TO (trailing columns are ignored), but coordinates are 0-based, half-open. To indicate that a file be treated as BED rather than the 1-based tab-delimited file, the file must have the '.bed' or '.bed.gz' suffix (case-insensitive). Uncompressed files are stored in memory, while bgzip-compressed and tabix-indexed region files are streamed. Note that sequence names must match exactly, 'chr20' is not the same as '20'. Also note that chromosome ordering in FILE will be respected, the VCF will be processed in the order in which chromosomes first appear in FILE. However, within chromosomes, the VCF will always be processed in ascending genomic coordinate order no matter what order they appear in FILE. Note that overlapping regions in FILE can result in duplicated out of order positions in the output. This option requires indexed VCF/BCF files. Note that -R cannot be used in combination with -r.
  type:
  - File
  - 'null'
  inputBinding:
    prefix: -R
- id: threads
  label: threads
  doc: |-
    Number of output compression threads to use in addition to main thread. Only used when --output-type is b or z. Default: 0.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --threads

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: generated.vcf.gz
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- bcftools
- concat
arguments: []

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