Canary is an efficient amplicon aligner, variant caller and annotator which transforms sequencer generated FASTQ files into VCF files annotated with HGVS nomenclature and Refseq transcripts. Implemented as a single JAR file, it is readily deployable onto any platform supporting a Java runtime. All variants identified by Canary are 3’ shifted and represented in their most parsimonious form to provide a consistent representation irrespective of how the reads represent base changes. Further, proximate in-phase variants are additionally represented as a single HGVS ‘delins’ variant. This allows for correct nomenclature and consequences to be ascribed to complex multi-nucleotide polymorphisms (MNPs) which are otherwise difficult to interpret.
Contact: Kenneth Doig email@example.com