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.