Tag: Variant Annotation

Vex-seq

[PMID: 29859120] [Genome Biology]

Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

“use to test the impact on pre-mRNA splicing of 2059 human genetic variants spanning 110 alternative exons.”

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VarAFT

[PMID: 29860484] [Nucleic Acids Research]

VarAFT: a variant annotation and filtration system for human next generation sequencing data

“VarAFT is a multiplatform freely available software that allows the simultaneous annotation, filtration, and breadth and depth of coverage analysis of WES, WGS and targeted sequencing experiments from any sequencing platform. Its graphical user interface, various modules and unique features, such as pathogenicity predictions from UMD-Predictor and HSF, allow untrained users to rapidly highlight disease-causing mutations in multiple genetic scenarios.”

PCGR

[PMID: 29272339] [Bioinformatics]

Personal Cancer Genome Reporter: variant interpretation report for precision oncology  

“The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual cancer genomes for precision oncology. It interprets both somatic SNVs/InDels and copy number aberrations. The software extends basic gene and variant annotations from the Ensembl’s Variant Effect Predictor (VEP) with oncology-relevant, up-to-date annotations retrieved flexibly through vcfanno, and produces interactive HTML reports intended for clinical interpretation.”