Fast somatic SNP Detector

Introduction


Recent advances in high-throughput sequencing technologies have enabled us to efficiently sequence large number of cancer samples to reveal novel insights into oncogenetic mechanisms. However, the presence of intratumoral heterogeneity, normal cells contamination and insufficient sequencing depth, together pose a challenge for detecting somatic mutations. Here we propose a fast and accurate somatic single-nucleotide variations detection program, FaSD-somatic, that combines the joint genotype likelihoods, and the FaSD score, which is previously defined in our lab. By comparison with several state-of-the-art somatic SNVs detection programs, the performance of FaSD-somatic is extensively assessed on various types of cancer. It is demonstrated that no matter the concordance with known somatic SNVs and non-somatic SNPs from database is applied as benchmark, or AUC with SNVs called from high depth data is used as benchmark, FaSD-somatic has the best performance. Furthermore, FaSD-somatic is the fastest somatic SNVs caller among current programs, and can finish calling somatic mutations in paired tumor and normal samples with 50X sequencing depth each within 14 hours.

The FaSD-somatic could be downloaded by clicking the hyperlinks: download here

You are welcome to discuss with us from FaSD Google Group

Please check the supplementary materials from here

Usage


Recommended input:

Run command: Multi-thread script for somatic SNVs calling in specified chromosomes: FaSD-somatic will output predicted somatic SNVs in the following TAB-delimited format:

Acknowledgments


Financial support was provided by Grants from the Research Grants Council (781511M, 778609M, N_HKU752/10) and Food and Health Bureau (10091262) of Hong Kong.
Conflict of interest statement. None declared.

Contact


*Correspondence should be addressed to Junwen Wang
(Tel: +852 2819 2809; Fax: +852 2855 1254)
(Email:
junwen@hku.hk ).
(Office: L3-80, Laboratory Block, 21 Sassoon Road, Hong Kong).