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SNVHMM: predicting single nucleotide variants from next generation sequencing

Jiawen Bian12, Chenglin Liu2, Hongyan Wang2, Jing Xing23, Priyanka Kachroo2 and Xiaobo Zhou4*

Author affiliations

1 School of Mathematics and Physics, China University of Geosciences, Wuhan 430074, China

2 Department of Radiology, The Methodist Hospital Research Institute, Weill Cornell Medical College, Houston 77030 TX, USA

3 Department of Statistics, Hubei University of Economics, Wuhan, 430025, China

4 Department of Diagnostic Radiology, Center for Bioinformatics & Systems Biology, Wake Forest University - School of Medicine, Winston-Salem 27103, NC, USA

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Citation and License

BMC Bioinformatics 2013, 14:225  doi:10.1186/1471-2105-14-225

Published: 15 July 2013



The rapid development of next generation sequencing (NGS) technology provides a novel avenue for genomic exploration and research. Single nucleotide variants (SNVs) inferred from next generation sequencing are expected to reveal gene mutations in cancer. However, NGS has lower sequence coverage and poor SNVs detection capability in the regulatory regions of the genome. Post probabilistic based methods are efficient for detection of SNVs in high coverage regions or sequencing data with high depth. However, for data with low sequencing depth, the efficiency of such algorithms remains poor and needs to be improved.


A new tool SNVHMM basing on a discrete hidden Markov model (HMM) was developed to infer the genotype for each position on the genome. We incorporated the mapping quality of each read and the corresponding base quality on the reads into the emission probability of HMM. The context information of the whole observation as well as its confidence were completely utilized to infer the genotype for each position on the genome in study. Therefore, more probability power can be gained over the Bayes based methods, which is very useful for SNVs detection for data with low sequencing depth. Moreover, our model was verified by testing against two sets of lobular breast tumor and Myelodysplastic Syndromes (MDS) data each. Comparing against a recently published SNVs calling algorithm SNVMix2, our model improved the performance of SNVMix2 largely when the sequencing depth is low and also outperformed SNVMix2 when SNVMix2 is well trained by large datasets.


SNVHMM can detect SNVs from NGS cancer data efficiently even if the sequence depth is very low. The training data size can be very small for SNVHMM to work. SNVHMM incorporated the base quality and mapping quality of all observed bases and reads, and also provides the option for users to choose the confidence of the observation for SNVs prediction.