controlsConfigTemplate.yaml

###input files
bamList:   BAMLIST      ###path to file contining path to bams
regionsFile: BEDFILE    ###path to bed file defining regions targeted in exome
refGenome: REFGENOME    ###path to reference genome that was used to align bams
snpVCFpath: VCFPATH     ###path to vcfs containg popuulation frequencies (one for each chromosome),
                        ###including part of filename before chromosome number
snpVCFname: VCFNAME     ###filename/extension of population vcf following chromosome number

###user inputs
sexList: SEXLIST        ###comma deliminated list of sex for each bam in the bamlist in the same order
gvmPath: GVMPATH        ###path to folder containing gvm executable
outfile: OUTFILE        ###path and name of output

###organism specific parameters
###values below are set for human
autosomes: "1:22"                                                                                 ####range of numbers for autosomal chromosmes 1:maxAutosome
sexChr: X,Y                                                                                     #### comma separated list of sex chromosomes
F: 2,0                                                                                          #### number of copies of sex chr for individuals of sex F
M: 1,1

###advanced parameters - most users should keep default belows below
mpileupC: 50                                                                                    ####mpileupC parameter
pvFreq: 1E-5                                                                                 ####expected frequency of private SNPs
pvFreqIndel: 1E-6                                                                            ####expected frequency of private indels
minMQ: 10                                                                                       ####minimum mapping quality to count read
defaultBQ: 30                                                                                   ####BQ used for indels
defaultMQ: 40
BQoffset: 33                                                                                    ####used for translation ascii to scores
MQoffset: 33                                                                                    ####used for translation ascii to score
priorMapError: 0.03                                                                             ####prior probability genotype cannot be determined at postion
                                                                                       #### number of copies of sex chr for individuals of sex M