BamQC
Introduction
From S. Andrews' lab, who also produce FastQC
Helpfile output
BamQC - A high throughput mapped sequence QC analysis tool
SYNOPSIS
bamqc bamfile1 .. bamfileN | <folder containing SAM/BAM mapped files>
bamqc [-o output dir] [--(no)extract] [-f file.gtf]
bamfile1 .. bamfileN | <folder containing SAM/BAM mapped files>
bamqc [-o output dir] [--(no)extract] [-g genome_dir]
bamfile1 .. bamfileN | <folder containing SAM/BAM mapped files>
bamqc [-o output dir] [--(no)extract] [-p species -e assembly]
bamfile1 .. bamfileN | <folder containing SAM/BAM mapped files>
DESCRIPTION
BamQC reads a set of mapped BAM files and produces from each one a quality
control report consisting of a number of different modules, each one of
which will help to identify a different potential type of problem in your
data.
If no files to process are specified on the command line then the program
will start as an interactive graphical application. If files are provided
on the command line then the program will run with no user interaction
required. In this mode it is suitable for inclusion into a standardised
analysis pipeline.
The options for the program as as follows:
-f --gff Use a specified annotation file as annotation set
-g --genome The directory containing species/assembly to use. If the
couple species assembly does not exist, BamQC will try to
download it.
-s --species The genome species to use. If the couple species assembly
does not exist, BamQC will try to download it.
-a --assembly The genome assembly associated to the species to use.
If the couple species assembly does not exist, BamQC
will try to download it.
-b --available [Pattern] List the genomes available on the Babraham Server
which are filtered using the string Pattern if this is provided.
This string is considered as a substring in the pattern matching.
For instance, the pattern=m?s will retrieve mus, mis, musculus,
humus. Therefore its behaviour is equivalent to *m?s*.
-e --saved List the saved genomes
-h --help Print this help file and exit
-v --version Print the version of the program and exit
-o --outdir Create all output files in the specified output directory.
Please note that this directory must exist as the program
will not create it. If this option is not set then the
output file for each sequence file is created in the same
directory as the sequence file which was processed.
--extract If set then the zipped output file will be uncompressed in
the same directory after it has been created. By default
this option will be set if bamqc is run in non-interactive
mode.
-j --java Provides the full path to the java binary you want to use to
launch bamqc. If not supplied then java is assumed to be in
your path.
--noextract Do not uncompress the output file after creating it. You
should set this option if you do not wish to uncompress
the output when running in non-interactive mode.
--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause bamqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
-l --limits Specifies a non-default file which contains a set of criteria
which will be used to determine the warn/error limits for the
various modules. This file can also be used to selectively
remove some modules from the output all together. The format
needs to mirror the default limits.txt file found in the
Configuration folder.
-q --quiet Supress all progress messages on stdout and only report errors.
-d --dir Selects a directory to be used for temporary files written when
generating report images. Defaults to system temp directory if
not specified.
