Best-practice variant calling pipeline for fully automated high throughput sequencing analysis
Authors: Chapman, Brad; Kirchner, Rory; Hofmann, Oliver; Hide, Winston
bcbio-nextgen is an automated, scalable pipeline for detecting genomic variants from large-scale next-generation sequencing data. It organizes multiple best-practice tools for alignment, post-processing and variant calling into a single, easily configurable pipeline. Users specify inputs and parameters in a configuration file and the pipeline handles all aspects of software and data management. Large-scale analysis run in parallel on compute clusters using IPython and on cloud systems using StarCluster. The goal is to create a validated and community maintained pipeline for automated variant calling, allowing researchers to focus on answering biological questions.
Our talk will describe the practical challenges we face in scaling the system to handle large whole genome data for thousands of samples. We will also discuss current work to develop a variant reference panel and associated grading scheme that ensures reproducibility in a research world with rapidly changing algorithms and tools. Finally we details plans for integration with STORMseq, a user-friendly Amazon front end, designed to make the pipeline available to non-technical users.
The presentation will show how bringing together multiple open-source communities provides infrastructure that bridges technical gaps and moves analysis work to higher-level challenges.