Tag Archives: GATK

The Genome Analysis Toolkit (GATK) is a popular set of programs for discovering and genotyping variants from next-generation sequencing data. The current GATK recommendation for RNA sequencing (RNA-seq) is to perform variant calling from individual ...

Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized ...

RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a ...

SAN DIEGO – PRNewswire – Edico Genome, creator of the world’s first bio-IT processor designed to analyze next-generation sequencing data, today announced a collaboration with IBM to make DRAGEN available on the new IBM Power Systems S822LC for high performance ...

This presentation was filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. For more information and to view other videos from the March 2015 GATK Workshop, please visit the GATK Workshop page.

SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot ...

RNA-Seq has become the method of choice to quantify genes and exons, discover novel transcripts, and detect fusion genes. However, reliable variant identification from RNA-Seq data remains challenging due to the complexities of the transcriptome, the challenges of accurately mapping ...

The Pipeline Challenge aims to select and reward a winning proposal for an innovative next-generation sequencing analysis pipeline. Any US-based researcher is eligible to enter the competition, which runs until August 15. The winner will receive $70,000 worth of bioinformatics ...

by Geraldine_VdAuwera at GATK Best Practices workflow for RNAseq This workflow is intended to be run per-sample; joint calling on RNAseq is not supported yet, though that is on our roadmap. Please see the new document here for full details ...

April 10, 2014 12 PM EDT Join Appistry for a live webinar exploring the new features in GATK 3. Geraldline Van der Auwera, moderator of the Broad Institute’s GATK forum and well known Voice of the GATK, will take a ...