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Arguments available to all methods

The following arguments are either required or available to use by all four methods: manipulateGTCs, createSampleSheet, getIntensities, sampleInformation

Argument	Defaults	Description
--bpm	required by user	Full path to bead pool manifest file (.bpm); must be same one used to generate gtc
--gtcDir	required by user	Full path to location of directory/folder containing gtc files to process (files must end in .gtc) -- will not recursively go into sub-directories
--outDir	optional, default=current working directory	Full path to directory or folder to output results. If it path does not exist, program will attempt to create it
--logName	optional, default=gtcFuncs.log	Name of log file to output, will be created in directory --outDir
--modDir	optional, default=current working directory	Full path to module files .py from github; default is current working directory with modules folder appended

Arguments specific to method: manipulateGTCs

In addition to the requirement of arguments --bpm and --gtcDir the following are also required/possible arguments to add at runtime specific to this method and an extension to the base argument options:

Argument	Defaults	Description
--updates	required by user	Full path to file containing snps and/or metadata to update. An example file can be found here or a detailed explanation can be found here.
--overrides	optional, default=None	a tab-delimited text file to temporarily update the snp listed in the bpm file (not GTC!), one snp per line, of snp name and allele change. Ex: rs12248560.1 [T/A], will update allele rs12248560.1 to have alleles T and A instead of what is listed on the bpm. An example file can be found here.

For more detailed information please read the manipulateGTCs wiki here. Schematics and detailed images and use are listed.

Arguments specific to method: createSampleSheet

In addition to the requirement of arguments --bpm and --gtcDir the following are also required/possible arguments to add at runtime specific to this method and an extension to the base argument options::

Argument	Defaults	Description
--config	required by user	Path and name to configuration file. An example file can be found here.
--sampleSheetUpdates	optional, default=None	Path and name of samplesheet updates. Tab-delimited with following headers required: patientName, DOB, sex, mrn, instrumentID. An example file can be found here.
--fileOutName	optional, default=sampleSheet.csv	Name of final samplesheet file to output, will be created in directory --outDir

For more detailed information please read the createSampleSheet wiki here. Schematics and detailed images and use are listed.

Arguments specific to method: sampleInformation

In addition to the requirement of arguments --bpm and --gtcDir the following are also possible arguments to add at runtime specific to this method and an extension to the base argument options::

Argument	Defaults	Description
--prefix	optional, default=None	string prefix to name image files, will be created in directory --outDir. If nothing is provided the following png files will be created and overwritten: callRatePlots.png, gc10Plots.png, logrDevPlots.png
--fileOutName	optional, default=allSampleInfo.txt	Name of final tab-delimited file to output, will be created in directory --outDir

For more detailed information please read the sampleInformation wiki here. Schematics and detailed images and use are listed.