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A genome-wide approach for detecting novel insertion-deletion variants of mid-range size. Nucleic acids research Xia, L. C., Sakshuwong, S., Hopmans, E. S., Bell, J. M., Grimes, S. M., Siegmund, D. O., Ji, H. P., Zhang, N. R. 2016; 44 (15)

Abstract

We present SWAN, a statistical framework for robust detection of genomic structural variants in next-generation sequencing data and an analysis of mid-range size insertion and deletions (<10 Kb) for whole genome analysis and DNA mixtures. To identify these mid-range size events, SWAN collectively uses information from read-pair, read-depth and one end mapped reads through statistical likelihoods based on Poisson field models. SWAN also uses soft-clip/split read remapping to supplement the likelihood analysis and determine variant boundaries. The accuracy of SWAN is demonstrated by in silico spike-ins and by identification of known variants in the NA12878 genome. We used SWAN to identify a series of novel set of mid-range insertion/deletion detection that were confirmed by targeted deep re-sequencing. An R package implementation of SWAN is open source and freely available.

View details for DOI 10.1093/nar/gkw481

View details for PubMedID 27325742

View details for PubMedCentralID PMC5009736