vcf.file = '/Users/leraman/PhD/BAF/batch1-gatk-haplotype-joint-annotated.vcf.gz'
singles = c('D1810466', 'D1810468', 'D1810470') # use for separate sample testing; will detect LOHs
trio = c() # use for trio analysis: father, mother, child; will detect LOH and increased mendelian errors (MEs)
output.dir = '/Users/leraman/PhD/BAF/output2'
cairo.bitmap = F # some systems require cairo bitmap for plotting
min.seq.depth = 15 # consider variants with at least a depth of min.seq.depth
hist.bins = 100 # number of bins in beta value histograms
bin.size = 5 # in MB, for LOH/ME calling
min.support = 1 # number of variants required in bin for P-value calculation; for LOH/ME calling
successive.bins.required = 3 # successive 'significant' bins required for actual significance of middle bin; for LOH/ME calling; odd number
cytoband = '/Users/leraman/PhD/BAF/cyotband.hg38.txt' # if given, filters out gvar and stalk