Changes in version 1.11.3: o Add hethom method to calculate heterozygosity / non-reference homozygosity in one step o Add countSingletons method Changes in version 1.11.1: o Add variantData slot to SeqVarData class Changes in version 1.9.11: o Add Firth test option to regression o Bug fix for refFracPlot: hets significantly different from 0.5 plotted as triangles, median line shown Changes in version 1.9.10: o duplicateDiscordance across two GDS files can calculate discordance based on heterozygote/homozygote status instead of genotype Changes in version 1.9.9: o duplicateDiscordance across two GDS files can match on either position or position and alleles, with the ability to recode genotypes if th reference allele in one dataset is the alternate allele in the other dataset Changes in version 1.9.8: o duplicateDiscordance and alternateAlleleDetection require SeqVarData objects; both can match on a subject.id instead of sample.id Changes in version 1.9.4: o alleleDosage returns list with dosage of each allele separately Changes in version 1.9.2: o added by.variant option to duplicateDiscordance for two gds files Changes in version 1.7.9: o added more options to return dosage of different alleles Changes in version 1.7.7: o added methods to calculate and plot reference allele fraction Changes in version 1.7.6: o HWE method returns additional columns and allows permutation of genotypes Changes in version 1.7.5: o Added SeqVarData class to combine sample annotation with GDS object Changes in version 1.7.4: o HWE works on biallelic INDELs as well as SNVs Changes in version 1.7.3: o Add methods for duplicateDiscordance with two datasets o Add alternateAlleleDetection Changes in version 1.5.1: o Use existing isSNV generic from VariantAnnotation instead of redefining o Use BiocStyle for vignette