cgpBigWig

Package of C scripts for generation of BigWig coverage files

| Master | Dev | |-----------------------------------------------|----------------------------------------------| | | |

• Installation
• Docker and Singularity
• Programs
  • bwcat
  • bwjoin
  • bam2bw
  • bg2bw
  • bam2bwbases
  • bam2bedgraph
• License

Installation

To install this package run:

setup.sh /path/to/installation

:warning: Be aware that this expects basic C compilation libraries and tools to be available, check the INSTALL for system specific dependencies (e.g. Ubuntu, OSX, etc.).

setup.sh will install the following external dependencies:

• libBigWig
• htslib

:warning: Please review the respective licence for each before use.

Docker and Singularity

A docker image for this tool can be found at quay.io (this may be more current than the dockstore version).

There are docker and dockstore.org containers for this project (including CWL bindings).

Programs

| Program | Description | | ----------------------------- | ------------------------------------------------------------------------- | | bwcat | Read the contents of a bigwig (.bw) file | | bwjoin | Concatenate bigwig files together | | bam2bw | Generate bigwig (.bw) coverage file from bam | | bg2bw | Generate bigwig (.bw) coverage file from bedgraph (.bed) format | | bam2bwbases | Generate bigwig (.bw) proportion file of each base at a position from bam | | bam2bedgraph | Generate a coverage bedgraph from bam |

bwcat

Read the contents of a bw file ``` Usage: bwcat -i input-path

-i --input-path [file] Path to the input bigwig file

Optional: -r --region [string] Region or bw file to print to screen format. NB start should be 0 based: (contig:start-stop) -n --include-na Include NA regions in output -o --output [file] File to write bw output to [default: stdout]

Other: -h --help Display this usage information. -v --version Prints the version number. ```

bwjoin

Concatenate bw files together ``` Usage: bwjoin -f genome.fai -o output.bw

-p --input-path [dir] Path to the input bigwig files named [path]/.bw -f --fasta-index [file] Fasta index file (.fai) -o --outfile [file] Path to the output .bw file produced. [default:'concatenated.bw'] -g --ignore-contigs [comma separated list] Comma separated list of contigs to ignore.

Other: -h --help Display this usage information. -v --version Prints the version number. ```

bam2bw

Generate bw coverage file from bam ``` Usage: bam2bw -i input.[b|cr]am -o output.bw bam2bw can be used to generate a bw file of coverage from a [cr|b]am file.

-i --input [file] Path to the input [b|cr]am file. -F --filter [int] SAM flags to filter. [default: 4] -f --filter-include [int] SAM flags to include. [default: 0] N.B. if properly paired reads are filtered for inclusion bam2bw will assume paired-end data and exclude any proper-pair flagged reads not in F/R orientation.-o --outfile [file] Path to the output .bw file produced. [default:'output.bam.bw']

Optional: -S --scale-log10 [float] A scale factor to multiply to output [default: -1912244352] -c --region [file] A samtools style region (contig:start-stop) or a bed file of regions over which to produce the bigwig file -z --include-zeroes Include zero coverage regions as additional entries to the bw file -r --reference [file] Path to reference genome.fa file (required for cram if ref_path cannot be resolved) -a --overlap Use overlapping read check

Other: -h --help Display this usage information. -v --version Prints the version number. ```

bg2bw

Generate bw coverage file from bedgraph (.bed) format ``` Usage: bg2bw -i input.bed -c chrom.list -o output.bw bg2bw can be used to generate a bw file from a bedgraph file.

-i --input [file] Path to the input [b|cr]am file. -o --outfile [file] Path to the output .bw file produced. [default:'output.bw'] -c --chromList [file] Path to chrom.list a .tsv where first two columns are contig name and length.

Other: -h --help Display this usage information. -v --version Prints the version number. ```

bam2bwbases

Generate bw proportion file of each base at a position from bam ``` Usage: bam2bwbases -i input.[b|cr]am -o output.bw bam2bwbases can be used to generate four bw files of per base proportions.

-i --input [file] Path to the input [b|cr]am file. -F --filter [int] SAM flags to filter. [default: 4] -o --outfile [file] Path to the output .bw file produced. Per base results wiillbe output as four bw files [ACGT].outputname.bw [default:'(null)'] -a --overlap Turn on overlaping reads check

Optional: -c --region [file] A samtools style region (contig:start-stop) or a bed file of regions over which to produce the bigwig file -r --reference [file] Path to reference genome.fa file (required for cram if ref_path cannot be resolved)

Other: -h --help Display this usage information. -v --version Prints the version number. ```

bam2bedgraph

Generate a coverage bedgraph from bam ``` Usage: bam2bedgraph -i input.[cr|b]am -o file [-r region] [-h] [-v]

Create a BEDGraph file of genomic coverage. BAM file must be sorted. -i --input Path to bam/cram input file. [default: stdin] -o --output File path for output. [default: stdout]

Optional: -r --region Region in bam to access. -f --filter Ignore reads with the filter flags [int]. -a --overlap Turn on overlaping reads check

Other: -h --help Display this usage information. -v --version Prints the version number. ```

Contributors

Thanks to the following contributors on dockstore-cgpbigwig which is now retired Michael R. Crusoe

License

``` Copyright (c) 2017-2018 Genome Research Ltd.

Author: David Jones cgphelp@sanger.ac.uk

This file is part of cgpBigWig.

cgpBigWig is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’." ```