Bina Bloggers

Free NGS Webinar: An Ensemble Approach with Machine Learning to Detect Cancer Variants

Posted by Jenny Hsu on May 12, 2016 10:00:00 AM


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Accurate detection of somatic mutations has proven to be challenging in cancer NGS analysis, due to tumor heterogeneity and cross-contamination between tumor and matched normal samples. Oftentimes, a somatic caller that performs well for one tumor may not for another.

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Topics: Somatic Mutation Detection, Bina Tools & Workflows, Webinar, Bina GMS, BioIT, SomaticSeq, NGS, VarScan, SomaticIndelDetector, VarDict, MuTect, SomaticSniper

VarDict: A Somatic Variant Caller Available in the Bina RAVE Software

Posted by Anoop Grewal on May 10, 2016 10:00:00 AM

somaticfinal.pngDetails 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 [1]. 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).

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Topics: DREAM Challenge Results, Somatic Mutation Detection, Tumor-Normal, Webinar, Bina RAVE, SomaticSeq, AstraZeneca, Sequencing, VarScan, JointSNVMix, SomaticIndelDetector, VarDict, MuTect, SomaticSniper

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