Improving bioinformatic pipelines for exome variant calling
Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
Genome Medicine 2012, 4:7 doi:10.1186/gm306Published: 30 January 2012
Exome sequencing analysis is a cost-effective approach for identifying variants in coding regions. However, recognizing the relevant single nucleotide variants, small insertions and deletions remains a challenge for many researchers and diagnostic laboratories typically do not have access to the bioinformatic analysis pipelines necessary for clinical application. The Atlas2 suite, recently released by Baylor Genome Center, is designed to be widely accessible, runs on desktop computers but is scalable to computational clusters, and performs comparably with other popular variant callers. Atlas2 may be an accessible alternative for data processing when a rapid solution for variant calling is required.