exampleConfig.yaml

expDesign :             individual_genetic_characteristics_design       # the experimental design tag
expDesignOntology :     MGED Ontology   # the experimental design term source reference (e.g. MGED, HUGO, etc.
expDesignFactorName :   somatic_variant # the experimental design factor name
expDesignFactorType :   disease_state   # the experimental design factor type
personLastName :        Radenbaugh      # the submitter's last name
personFirstName :       Amie            # the submitter's first name
personMidInitial :      J               # the submitter's middle initial
personEmail :           aradenba@soe.ucsc.edu   # the submitter's email
personAddress :         University of California Santa Cruz, 1156 High St, Mail Stop CBSE, Santa Cruz, CA 95064, USA    # the submitter's institutional address
personAffiliation :     University of California Santa Cruz Genome Institute    # the submitter's affiliation
personRole :            submitter       # the submitter's role
pubMedId :              25405470        # the PubMed ID
pubAuthors :            Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D        # the publication author list
pubTitle :              'RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection'   # the publication title, quotes needed to escape colon
pubStatus :             published       # the publication status
expDescription :        Detection of somatic variants from the TCGA Whole-Exome Sequencing (WES) and RNA-Seq data using RADIA   # the description of the experiment
protocolNames :         ucsc.edu:variant_calling:Illumina_DNASeq:01 # the protocol names
protocolTypes :         Variant Calling # the protocol types
protocolDescriptions :  Somatic Variant Calling Pipeline:RADIA v1.1.1 (https://github.com/aradenbaugh/radia/),Annotation:SnpEff v3.3_GRCh37.69 (http://snpeff.sourceforge.net/)       # the protocol descriptions
protocolOntologies :    MGED Ontology,MGED Ontology     # the protocol ontologies
protocolParameters :    NA              # the protocol parameters
ontologyName :          MGED Ontology   # the ontology name
ontologyFile :          http://mged.sourceforge.net/ontologies/MGEDontology.php # the ontology file
ontologyVersion :       1.3.1.1         # the ontology version