Svviz：用于验证结构变异的读取查看器。

svviz: a read viewer for validating structural variants.

作者信息

Spies Noah, Zook Justin M, Salit Marc, Sidow Arend

机构信息

Department of Genetics, Stanford University, Department of Pathology, Stanford University, Genome Scale Measurements Group, National Institute of Standards and Technology, Stanford, CA, USA and.

Genome Scale Measurements Group, National Institute of Standards and Technology, Gaithersburg, MD, USA.

出版信息

Bioinformatics. 2015 Dec 15;31(24):3994-6. doi: 10.1093/bioinformatics/btv478. Epub 2015 Aug 18.

DOI:10.1093/bioinformatics/btv478

PMID:26286809

Abstract

UNLABELLED

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms.

AVAILABILITY AND IMPLEMENTATION

svviz is implemented in python and freely available from http://svviz.github.io/.

摘要

未标注

可视化读取比对是利用现有数据验证候选结构变异（SV）的最有效方法。我们展示了svviz，这是一种用于SV的测序读取可视化工具，它仅对与候选SV相关的读取进行排序和显示。svviz的工作方式是在输入的bam文件中搜索潜在相关的读取，将它们与推定变异等位基因以及参考等位基因的推断序列重新比对，并识别与一个等位基因比对优于另一个等位基因的读取。然后，在可滚动的网页浏览器视图中显示两个等位基因的单独视图，与大多数当前读取浏览器常见的基于单参考基因组的视图相比，能够更直观地可视化每个等位基因。浏览器视图有助于检查支持或反对推定变异的证据、估计纯合度、可视化受影响的基因组注释以及手动优化断点。svviz支持来自大多数现代测序平台的数据。