Details on Vardict, a new variant caller, have been published recently in Nucleic Acids Research by authors, Zhongwu Lai and Jonathan Dry, among others from AstraZeneca . The current version of the Bina Read Alignment Variant Calling and Expression software module for secondary analysis includes Vardict, along with five other tools, for calling SNVs or indels from tumor-normal pairs. As the article demonstrates, VarDict has multiple strengths that extend our capabilities in variant calling beyond what was available before its release. Notably, the algorithm is particularly good at detecting indels. It also handles ultra-deep sequenced samples, which have become more common of late, and supports variant calling in tumor-only samples (in addition to tumor-vs-normal calling).
Topics: DREAM Challenge Results, Somatic Mutation Detection, Tumor-Normal, Webinar, Bina RAVE, SomaticSeq, AstraZeneca, Sequencing, VarScan, JointSNVMix, SomaticIndelDetector, VarDict, MuTect, SomaticSniper
The Roche “Assembling the Puzzle” Workshop featured three amazing speakers from academia and industry: Kim Doheny, Director of the Center for Inherited Disease Research (CIDR) from Johns Hopkins, Kristine Wylie, Professor of Pediatrics from Washington University, as well as the Director of Development at Nimblegen, Dan Burgess. Each speaker explained how various Roche Sequencing solutions are being used to advance studies spanning metagenomic viral profiling to human whole genome analysis.
In cancer research, it is common to search for somatic mutations that appear in the tumor but not in the healthy tissues. Thus, tumor-normal comparisons have become the norm in somatic mutation detection in DNA sequencing. In an ideal world the workflow sounds simple: compare the tumor sequencing data against the normal. If a variant was found in the tumor but not found in the normal, it’s a somatic mutation.