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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

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hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.

Meng Wang¹, Keith M Callenberg², Raymond Dalgleish³

¹School of Life Sciences, Peking University, Beijing, China.

|August 22, 2018

Summary

This summary is machine-generated.

The hgvs Python package ensures accurate human genome variation Society (HGVS) nomenclature for DNA, RNA, and protein variants. This tool standardizes variant reporting and interpretation, crucial for clinical settings.

Keywords:

HGVS clinvar sequence variant variant representation

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Accurate description of sequence variants is vital for public databases and scientific literature.
Inconsistent application of Human Genome Variation Society (HGVS) nomenclature can lead to clinical misinterpretations.
Reliable software is essential for consistent HGVS guideline adherence in variant reporting.

Purpose of the Study:

To introduce the hgvs Python package, a tool for manipulating sequence variants according to HGVS nomenclature.
To highlight recent updates and extensive validation of the hgvs package.

Main Methods:

Development of a comprehensive Python package for parsing, formatting, validating, and normalizing sequence variants.
Implementation of variant projection between aligned sequences, including gapped alignments.
Flexible installation options (remote/local) and extensive automated testing.

Main Results:

The hgvs package supports genome, transcript, and protein sequence variants.
It enables projection of variants across different sequence alignments.
Validation using clinical variants from ClinVar and HGMD demonstrates reliability.

Conclusions:

The hgvs Python package provides a robust solution for consistent HGVS nomenclature application.
Its features facilitate accurate variant interpretation in research and clinical contexts.
Open-source development ensures ongoing improvement and community support.