scReadCounts extracts VAF matrices for single-cell sequencing workflows from reads labelled with cell-barcodes.

readCounts tabulates the read-counts in support of variant and reference nucleotides at specific genomic loci and applies statistical tests to recognize allelic read-counts consistent with homozygous and heterozygous loci.

RNA2DNAlign evaluates evidence for asymmetric allele distribution in next-gen sequencing reads of DNA and RNA samples from the same individual.

SNPlice finds and evaluates the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.