|--basename=BASE||BASE will be used to name all the output files produced by Birdsuite.|
|--chipType=CHIP_TYPE||CHIP_TYPE This is used to select the appropriate metadata files corresponding to the Affy chip. Currently only GenomeWideSNP_6 and GenomeWideSNP_5 are supported.|
|--genderFile=GENDER_FILE||The gender file must align with the list of cel files passed to Birdsuite. It must contain a header line "gender", and then a line for each cel file, with 0 representing female, 1 representing male, and 2 representing unknown.|
Cel files may be specified by enumerating them on the command line, or putting the list of files into a file with header line "cel_files", and specifying this file on the command line with option --celFiles.
Use a specific models file to aid in clustering common copy-number polymorphism. For example, setting this option t:
will result in better clustering for samples of European ancestry. The default is a models file built using all 270 HapMap samples.
|--canary.allele_freq_weight=WEIGHT||How much to weight observed CNP frequency from HapMap to aid in clustering. The recommended value is 32 if samples are of European ancestry and one is using the GenomeWideSNP_6.CEU.canary_priors models file.|
|--outputDir=OUTPUTDIR||Write outputs somewhere other than the current directory.|
|--genomeBuild=GENOME_BUILD||Use the specified genome build. hg18 is the default. Currently hg17 and hg18 are supported. This option has both direct and indirect effect. The direct effect is that Birdseye calls will be relative to the specified genome build. The indirect effects are due to the fact that a probe may be considered part of a CNP in one build but not the other, which may result in changes in the way a probe is handled by Birdseed, Birdseye and Larry Bird.|
|--apt_probeset_summarize.force||Passed through to apt_probeset_summarize. Use this option if one or more of the cel files was processed with a non-standard CDF.|
|--noLsf||By default Birdsuite use the Load-Sharing Facility (LSF) to parallelize parts of the Birdsuite pipeline. Use this option if you do not have LSF installed on your system, or do not wish to use LSF.|
|--firstStep and --lastStep tell Birdsuite what stage of the pipeline to start and stop at. They are typically used only for debugging.
birdsuite.sh -hto see the list of steps.
|--exeDir and --metadataDir tell Birdsuite where to find executables and metadata. If you have set up your installation according to the installation instructions, you should not need to supply these options.|
|--configFile=CONFIG_FILE||This is a convenient way to organize options so as not to have to type them into the command line each time. Each line in the config file should be of ther form OPTION=VALUE just as on the command line, except without the --. Settings in the config file are overridden by those specified on the command line. We provide some premade config files that have been optimized for certain common study types; check the meta data directory for birdsuite_config files to see if your specific population and chip are supported. For samples of European ancestry, we recommend using the included file GenomeWideSNP_6.CEU.birdsuite_config (or setting the values canary.priors and canary.allele_freq_weight as suggested above.)|