GASV & GASVPro: Geometric Analysis of Structural Variants. GASV and GASVPro are software packages for analysis of structural variation from paired-end sequencing and/or array-CGH data. This software has been tested used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format. GASVPro is a probabilistic version of our original GASV algorithm. GASVPro combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation. When multiple alignments of a read are given, GASVPro utilizes a Markov Chain Monte Carlo procedure to sample over the space of possible alignments.

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  1. Kim, Jongkyu; Reinert, Knut: Vaquita: fast and accurate identification of structural variation using combined evidence (2017)
  2. Sindi, Suzanne S.; Helman, Elena; Bashir, Ali; Raphael, Benjamin J.: A geometric approach for classification and comparison of structural variants (2009) ioport