VariantClassifier: A hierarchical variant classifier for annotated genomes.

BMC Research Notes
Kelvin Li, Timothy B Stockwell

Abstract

High-throughput DNA sequencing has produced a large number of closed and well annotated genomes. As the focus from whole genome sequencing and assembly moves towards resequencing, variant data is becoming more accessible and large quantities of polymorphisms are being detected. An easy-to-use tool for quickly assessing the potential importance of these discovered variants becomes ever important. Written in Perl, the VariantClassifier receives a list of polymorphisms and genome annotation, and generates a hierarchically-structured classification for each variant. Depending on the available annotation, the VariantClassifier may assign each polymorphism to a large variety of feature types, such as intergenic or genic; upstream promoter region, intronic region, exonic region or downstream transcript region; 5' splice site or 3' splice site; 5' untranslated region (UTR), 3' UTR or coding sequence (CDS); impacted protein domain; substitution, insertion or deletion; synonymous or non-synonymous; conserved or unconserved; and frameshift or amino acid insertion or deletion (indel). If applicable, the truncated or altered protein sequence is also predicted. For organisms with annotation maintained at Ensembl, a software application for d...Continue Reading

References

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Citations

Mar 12, 2013·Genome Biology and Evolution·Laura E Williams, Jennifer J Wernegreen
Jun 13, 2012·Nucleic Acids Research·Ngak-Leng SimPauline C Ng
Aug 11, 2015·Nature·Ronen DurstSusan A Slaugenhaupt
May 14, 2011·American Journal of Human Genetics·Laura SouthgateRichard C Trembath

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Software Mentioned

Ensembl
VariantClassifier
SIFT
Linux
Perl
OpenOffice Calc
Microsoft Excel
BLOck SUbstitution Matrix ( BLOSUM )

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