cleanVariants           Check provided variants for compatibility
digestSalmon            Parse the output from salmon
genomogrify             Mogrify a genome using a set of variants
indelcator              Substitute InDels into one or more sequences
overlapsByVar           Count overlaps by variant type
owl                     OverWrite Letters in an XStringSet
parY                    Get the PAR-Y Regions From a Seqinfo Object
shiftByVar              Calculate new exon co-ordinates
sjFromExons             Obtain Splice-Junctions from Exons and
                        Transcripts
transmogrify            Mogrify a transcriptome using a set of variants
upsetVarByCol           Show Variants by Impacted Columns
varTags                 Create a set of tags indicating overlap status
                        with variants
varTypes                Identify SNVs, Insertions and Deletions
