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cgpBigWig

Package of C scripts for generation of BigWig coverage files

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Installation

To install this package run:

setup.sh /path/to/installation

⚠️ 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:

⚠️ 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]/<contig_name>.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 <[email protected]>

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’."