Package of C scripts for generation of BigWig coverage files
| Master | Dev |
|---|---|
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To install this package run:
setup.sh /path/to/installation
INSTALL for system specific dependencies (e.g. Ubuntu, OSX, etc.).
setup.sh will install the following external dependencies:
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).
| 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 |
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.
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.
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.
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.
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.
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.
Thanks to the following contributors on dockstore-cgpbigwig which is now retired
Michael R. Crusoe
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’."
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