ADnorm                  Normalized allele depth example data
ADtable                 Allele Depth (AD) example data
ad.correct              Correct allele depth values
allele.freq             Generate allele frequency table for individuals
                        or populations
allele.info             Get allele information for duplicate detection
alleleINF               Allele info example data
cnv                     Find CNVs from deviants
cpm.normal              Calculate normalized depth for alleles
depthVsSample           Simulate median allele ratios for varying
                        number of samples and depth values
dup.plot                Plot classified SNPs into deviants/CNVs and
                        non-deviants/non-CNVs
dup.validate            Validate detected deviants/cnvs
dupGet                  Detect deviants from SNPs; classify SNPs
exportVCF               Export VCF files
get.miss                Get missingness of individuals in raw vcf
gt.format               Format genotype for BayEnv and BayPass
h.zygosity              Determine per sample heterozygosity and
                        inbreeding coefficient
hetTgen                 Generate allele depth or genotype table
maf                     Remove MAF allele
norm.fact               Calculate normalization factor for each sample
power.bias              Simulate and plot detection power of bias in
                        allele ratios
readVCF                 Import VCF file
relatedness             Determine pairwise relatedness
sig.hets                Identify significantly different heterozygotes
                        from SNPs data
sim.als                 Simulate Allele Frequencies
vcf.stat                Get sequencing quality statistics of raw VCF
                        files (with GatK generated vcf files only)
vst                     Calculate population-wise Vst
vstPermutation          Run permutation on Vst
