toy.json

{
    // database in this block used to predict variant types and HGVS names
    "hgvs": {        
	"gene_data":"example/toy.gea.gz", // GenePredExt format is defined by bcfanno, check manual for details
        "refseq":"example/toy_transcripts.fa", // whole sequences of transcripts
        "columns":"MolecularConsequence,ExonIntron,Gene,Transcript,HGVSnom,AAlength",
        //"trans_list":"trans.list",
    },
    // allele specific databases
    "vcfs": [
        // dbSNP database
        {
            "file":"example/toy_dbsnp.bcf",
            "columns":"DBSNP_ASP,DBSNP_ASS,DBSNP_CAF,DBSNP_CFL,CLNDBN,CLNDSDB,CLNORIGIN,CLNSIG,DBSNP_COMMON,DBSNP_DSS,RS,DBSNP_SAO,DBSNP_VLD,DBSNP_VP",
        },
        //  HGMD database
        {
            "file":"example/toy_hgmd.bcf",
            "columns":"HGMD_disease,HGMD_tag,HGMD_pmid,HGMD_acc_num,HGMD_descr",
        },
    ],
    // region sepecific databases
    "beds": [
        { 
            "file": "example/toy_cytoband.bed.gz", // for bed-like database, self-defined header should be set at the beginning of this file.
            "columns": "CytoBand",
        },
    ],
}