“The Broad Institute has described GATK 3 as a shift in the way they approach problems in NGS data analysis, as well as a shift in the scope of problems the toolkit can tackle,” said Trevor Heritage, vice president of corporate development and strategy at Appistry. For instance, a collection of enhancements to the GATK speeds the analysis of the large sample sets typically associated with observational clinical studies (cohorts). This is accomplished through two main updates:
- An optimized algorithm achieved through a collaboration between the Broad Institute and Intel. The Broad says the optimization will enable scientists to conduct variant discovery three to five times faster than with prior versions of the GATK and to analyze a whole genome in one day rather than three.
- A new pipeline that better supports large, multi-sample analysis. Rather than re-calling data for all samples in a study when new samples are added, scientists can now analyze the new samples as they are sequenced and combine these results with the stored results from the rest of the cohort.
Additionally, the GATK for the first time includes best-practice recommendations for calling variants from RNA sequencing, which has emerged as a critical source of information on cellular function and activity. The initial best practices focus on data processing and variant calling steps; recommendations for other key analysis steps will be introduced in future releases.
Read more at http://www.broadwayworld.com/bwwgeeks/article/Appistry-Releases-Commercial-Version-of-Broad-Institutes-GATK-3-20140403#Ii83rZScvv9whF3o.99
