GLtoGP                  Convert genotype likelihoods to genotype
                        probabilities
PROVEANDb-class         PROVEANDb objects
PolyPhenDb-class        PolyPhenDb objects
PolyPhenDbColumns       PolyPhenDb Columns
SIFTDb-class            SIFTDb objects
SIFTDbColumns           SIFTDb Columns
ScanVcfParam-class      Parameters for scanning VCF files
VCF-class               VCF class objects
VCFHeader-class         VCFHeader instances
VRanges-class           VRanges objects
VRangesList-class       VRangesList objects
VariantAnnotation-defunct
                        Defunct Functions in Package
                        'VariantAnnotation'
VariantType-class       VariantType subclasses
VcfFile                 Manipulate Variant Call Format (Vcf) files.
filterVcf               Filter VCF files
genotypeToSnpMatrix     Convert genotype calls from a VCF file to a
                        SnpMatrix object
getTranscriptSeqs       Get transcript sequences
indexVcf                Create index files for VCF files
isSNV                   Identification of genomic variant types.
locateVariants          Locate variants
post_Hs_region          elementary vep/homo_sapiens/region call to
                        ensembl VEP REST API
predictCoding           Predict amino acid coding changes for variants
probabilityToSnpMatrix
                        Convert posterior genotype probability to a
                        SnpMatrix object
readVcf                 Read VCF files
scanVcf                 Import VCF files
seqinfo                 Get seqinfo for VCF file
snpSummary              Counts and distribution statistics for SNPs in
                        a VCF object
summarizeVariants       Summarize variants by sample
variant_body            helper function to construct inputs for VEP
                        REST API
vep_by_region           Use the VEP region API on variant information
                        in a VCF object as defined in
                        VariantAnnotation.
writeVcf                Write VCF files
