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Improving bioinformatic pipelines for exome variant calling

Hanlee P Ji

Author Affiliations

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/gm306

Published: 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.

See research article webcite.

Next-generation sequencing; exomes; variant calling; single nucleotide variation; insertion; deletions