HGVS Parser, Formatter, Mapper, Validator
Genome, transcript, and protein sequence variants are typically reported using the mutation nomenclature (“mutnomen”) recommendations provided by the Human Genome Variation Society (HGVS). This standard was formulated in an era of specialized sequencing and cytogenetic analyses, long before high-throughput sequencing annotation was envisioned. Unfortunately, the complexity of biological phenomena and the breadth of the standard makes it difficult to implement the standard in software.
This package, hgvs, is an easy-to-use Python library for parsing, representing, formatting, and mapping variants between genome, transcript, and protein sequences. The current implementation handles most (but not all) of the standard for precisely defined sequence variants. The intent is to centralize the subset of HGVS variant manipulation that is routinely used in modern, high-throughput sequencing analysis.
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