BEDTools: coverageBed¶
bedtoolsCoverageBed · 1 contributor · 1 version
The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that bedtools coverage offers is that it not only counts the number of features that overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus, bedtools coverage also computes the breadth of coverage observed for each interval in A.
Quickstart¶
from janis_bioinformatics.tools.bedtools.coveragebed.versions import BedToolsCoverageBed_2_29_2 wf = WorkflowBuilder("myworkflow") wf.step( "bedtoolscoveragebed_step", BedToolsCoverageBed_2_29_2( inputABed=None, inputBBam=None, ) ) wf.output("out", source=bedtoolscoveragebed_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 bedtoolsCoverageBed:
# user inputs
janis inputs bedtoolsCoverageBed > inputs.yaml
inputs.yaml
inputABed: inputABed.bed
inputBBam: inputBBam.bam
- Run bedtoolsCoverageBed with:
janis run [...run options] \
--inputs inputs.yaml \
bedtoolsCoverageBed
Information¶
| ID: | bedtoolsCoverageBed |
|---|---|
| URL: | https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html |
| Versions: | v2.29.2 |
| Container: | quay.io/biocontainers/bedtools:2.29.2–hc088bd4_0 |
| Authors: | Jiaan Yu |
| Citations: | None |
| Created: | 2020-02-20 |
| Updated: | 2020-02-26 |
Outputs¶
| name | type | documentation |
|---|---|---|
| out | stdout<TextFile> |
Additional configuration (inputs)¶
| name | type | prefix | position | documentation |
|---|---|---|---|---|
| inputABed | bed | -a | input file a: only bed is supported. May be followed with multiple databases and/or wildcard (*) character(s). | |
| inputBBam | BAM | -b | input file b: only bam is supported. | |
| strandedness | Optional<Boolean> | -s | Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand. | |
| differentStrandedness | Optional<Boolean> | -S | Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand. | |
| fractionA | Optional<Float> | -f | Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) | |
| fractionB | Optional<Float> | -F | Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50) | |
| reciprocalFraction | Optional<Boolean> | -r | Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B. | |
| minFraction | Optional<Boolean> | -r | Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. | |
| split | Optional<Boolean> | -split | Treat ‘split’ BAM or BED12 entries as distinct BED intervals. | |
| genome | Optional<File> | -g | Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option. | |
| noNameCheck | Optional<Boolean> | -nonamecheck | For sorted data, don’t throw an error if the file has different naming conventions for the same chromosome. ex. ‘chr1’ vs ‘chr01’. | |
| sorted | Optional<Boolean> | -sorted | Use the ‘chromsweep’ algorithm for sorted (-k1,1 -k2,2n) input. | |
| header | Optional<Boolean> | -header | Print the header from the A file prior to results. | |
| noBuf | Optional<Boolean> | -nobuf | Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time. | |
| bufMem | Optional<Integer> | -iobuf | Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files. | |
| histogram | Optional<Boolean> | -hist | Report a histogram of coverage for each feature in A as well as a summary histogram for _all_ features in A. Output (tab delimited) after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth. | |
| depth | Optional<Boolean> | -d | Report the depth at each position in each A feature. Positions reported are one based. Each position and depth follow the complete A feature. | |
| counts | Optional<Boolean> | -counts | Only report the count of overlaps, don’t compute fraction, etc. | |
| mean | Optional<Boolean> | -mean | Report the mean depth of all positions in each A feature. |
Workflow Description Language¶
version development
task bedtoolsCoverageBed {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
Boolean? strandedness
Boolean? differentStrandedness
Float? fractionA
Float? fractionB
Boolean? reciprocalFraction
Boolean? minFraction
Boolean? split
File? genome
Boolean? noNameCheck
Boolean? sorted
Boolean? header
Boolean? noBuf
Int? bufMem
File inputABed
File inputBBam
Boolean? histogram
Boolean? depth
Boolean? counts
Boolean? mean
}
command <<<
set -e
coverageBed \
~{if (defined(strandedness) && select_first([strandedness])) then "-s" else ""} \
~{if (defined(differentStrandedness) && select_first([differentStrandedness])) then "-S" else ""} \
~{if defined(fractionA) then ("-f " + fractionA) else ''} \
~{if defined(fractionB) then ("-F " + fractionB) else ''} \
~{if (defined(reciprocalFraction) && select_first([reciprocalFraction])) then "-r" else ""} \
~{if (defined(minFraction) && select_first([minFraction])) then "-r" else ""} \
~{if (defined(split) && select_first([split])) then "-split" else ""} \
~{if defined(genome) then ("-g '" + genome + "'") else ""} \
~{if (defined(noNameCheck) && select_first([noNameCheck])) then "-nonamecheck" else ""} \
~{if (defined(sorted) && select_first([sorted])) then "-sorted" else ""} \
~{if (defined(header) && select_first([header])) then "-header" else ""} \
~{if (defined(noBuf) && select_first([noBuf])) then "-nobuf" else ""} \
~{if defined(bufMem) then ("-iobuf " + bufMem) else ''} \
-a '~{inputABed}' \
-b '~{inputBBam}' \
~{if (defined(histogram) && select_first([histogram])) then "-hist" else ""} \
~{if (defined(depth) && select_first([depth])) then "-d" else ""} \
~{if (defined(counts) && select_first([counts])) then "-counts" else ""} \
~{if (defined(mean) && select_first([mean])) then "-mean" else ""}
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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: 'BEDTools: coverageBed'
doc: |-
The bedtools coverage tool computes both the depth and breadth of coverage of features in file B on the features in file A. For example, bedtools coverage can compute the coverage of sequence alignments (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. One advantage that bedtools coverage offers is that it not only counts the number of features that overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features. Thus, bedtools coverage also computes the breadth of coverage observed for each interval in A.
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0
inputs:
- id: strandedness
label: strandedness
doc: |-
Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand.
type:
- boolean
- 'null'
inputBinding:
prefix: -s
- id: differentStrandedness
label: differentStrandedness
doc: |-
Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand.
type:
- boolean
- 'null'
inputBinding:
prefix: -S
- id: fractionA
label: fractionA
doc: |-
Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
type:
- float
- 'null'
inputBinding:
prefix: -f
- id: fractionB
label: fractionB
doc: |-
Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
type:
- float
- 'null'
inputBinding:
prefix: -F
- id: reciprocalFraction
label: reciprocalFraction
doc: |-
Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B.
type:
- boolean
- 'null'
inputBinding:
prefix: -r
- id: minFraction
label: minFraction
doc: |-
Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied.
type:
- boolean
- 'null'
inputBinding:
prefix: -r
- id: split
label: split
doc: Treat 'split' BAM or BED12 entries as distinct BED intervals.
type:
- boolean
- 'null'
inputBinding:
prefix: -split
- id: genome
label: genome
doc: |-
Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option.
type:
- File
- 'null'
inputBinding:
prefix: -g
- id: noNameCheck
label: noNameCheck
doc: |-
For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. 'chr1' vs 'chr01'.
type:
- boolean
- 'null'
inputBinding:
prefix: -nonamecheck
- id: sorted
label: sorted
doc: Use the 'chromsweep' algorithm for sorted (-k1,1 -k2,2n) input.
type:
- boolean
- 'null'
inputBinding:
prefix: -sorted
- id: header
label: header
doc: Print the header from the A file prior to results.
type:
- boolean
- 'null'
inputBinding:
prefix: -header
- id: noBuf
label: noBuf
doc: |-
Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time.
type:
- boolean
- 'null'
inputBinding:
prefix: -nobuf
- id: bufMem
label: bufMem
doc: |-
Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files.
type:
- int
- 'null'
inputBinding:
prefix: -iobuf
- id: inputABed
label: inputABed
doc: |-
input file a: only bed is supported. May be followed with multiple databases and/or wildcard (*) character(s).
type: File
inputBinding:
prefix: -a
- id: inputBBam
label: inputBBam
doc: 'input file b: only bam is supported.'
type: File
inputBinding:
prefix: -b
- id: histogram
label: histogram
doc: |-
Report a histogram of coverage for each feature in A as well as a summary histogram for _all_ features in A. Output (tab delimited) after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth.
type:
- boolean
- 'null'
inputBinding:
prefix: -hist
- id: depth
label: depth
doc: |-
Report the depth at each position in each A feature. Positions reported are one based. Each position and depth follow the complete A feature.
type:
- boolean
- 'null'
inputBinding:
prefix: -d
- id: counts
label: counts
doc: Only report the count of overlaps, don't compute fraction, etc.
type:
- boolean
- 'null'
inputBinding:
prefix: -counts
- id: mean
label: mean
doc: Report the mean depth of all positions in each A feature.
type:
- boolean
- 'null'
inputBinding:
prefix: -mean
outputs:
- id: out
label: out
type: stdout
stdout: _stdout
stderr: _stderr
baseCommand:
- coverageBed
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: bedtoolsCoverageBed