qProfiler2

qprofiler2 is a standalone Java app that takes in BAM, FASTQ, VCF files and provides an XML file containing basic summary statistics for each file. It is a newer version of qProfiler but with more features.

System Requirements

• Java 1.8
• Multi-core machine (ideally) and 10GB of RAM

Usage

java -jar qprofiler2-all-2.0.jar -h

usage: qprofiler [option...] --log logfile --loglevel INFO --output outputfile --input inputfile [-ntP 4 -ntC 16] 

Option                  Description                           
-------------------------------------------------                          
--format                classify vcf counts according to user specified format fields. Example values are "CCM", "INF", "FT=PASS", etc.                               
--fullBamHeader         If this option is set, whole BAM header will be ouputed into XML file; otherwise only HD and SQ will be outputted.                       
--help                  Shows this help message.            
--index                 File containing index data relating to primary input file                 
--input                 File containing data to be profiled (currently limited to BAM/SAM,FASTQ, VCF)       
--log                   File where log output will be directed (must have write permissions)       
--loglevel              Logging level required, e.g. INFO,DEBUG. (Optional) If no parameter is specified, will default to INFO    
--maxRecords <Integer>  Only process the first {0} records in the BAM file.                       
--ntConsumer <Integer>  specify how many threads should be used when processing the input file  (BAM files only)                    
--ntProducer <Integer>  specify how many threads should be    
--output                File where the output of the qprofiler should be written to (needs to be an xml file)                           
--validation            How strict to be when reading a SAM or BAM. Possible values: {STRICT, LENIENT, SILENT}                    
--version               Print version info.    

NOTE:

• The BWA mapped bam files may need to be run with the optional parameter -validation SILENT otherwise Picard will throw an exception.
• If no output file is specified (a supplied file with a .xml extension is considered an output file), then the process will write to a default file (currently qprofiler.xml).