From S. Andrews' lab, who also produce FastQC
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.