Our Services

VANGARD provides standard analysis for RNA-Seq, DNA-Seq, ChIP-Seq, and GRO/PRO-Seq, which implements "best practices" pipeline for the sequencing data provided.


DNA-Seq Analysis

The goal is to call variants or somatic mutations. DNA-seq data are mapped to the reference genome using BWA1, variants are called using GATK2 Best practice, somatic mutation are identified by Mutect3, and variants/somatic mutations are functionally annotated by ANNOVAR4. VANGARD will perform quality check, including raw reads quality (reads QC), mapping quality (mapping QC) to ensure high quality results.

DNA-seq pipeline


1. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
2. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res, 20, 1297-1303.
3. Cibulskis, K., Lawrence, M.S., Carter, S.L., Sivachenko, A., Jaffe, D., Sougnez, C., Gabriel, S., Meyerson, M., Lander, E.S. and Getz, G. (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol, 31, 213-219.
4. Wang, K., Li, M. and Hakonarson, H. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res, 38, e164.