SAAS-CNV is a tool to identify somatic copy number variation (CNV) in next-generation sequencing (NGS) data. The SAAS-CNV algorithm consists of four main steps: (1) reading a reference and alleles at each locus for comparison of the read depth and alleles with tumor and healthy samples, (2) joint segmentation on the two signals, (3) correction of the CNV baseline, (4) calling of somatic CNVs for all detected signals.
Genetics; DNA structural variation; Oncology
Zhang Z, Hao K "SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data." PLoS Comput Biol. 2015 Nov 19;11(11):e1004618. eCollection 2015 Nov. https://doi.org/10.1371/journal.pcbi.1004618
Zhang Z, Hao K "Using SAAS-CNV to Detect and Characterize Somatic Copy Number Alterations in Cancer Genomes from Next Generation Sequencing and SNP Array Data." Methods Mol Biol. 2018;1833:29-47. https://doi.org/10.1007/978-1-4939-8666-8_2
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