A tool to call copy-number variation (CNV) with ADAM and Apache Spark. The DECA algorithm implements XHMM, including new optimizations, to speed up the computation. It also uses the Viterbi algorithm in logs space and scaled versions of the forward and backward algorithms. Requires: Maven, Spark 2.1.0+, Hadoop 2.7, Scala 2.11.
DNA structural variation; Genetic variation;
Linderman MD, Chia D, Wallace F, Nothaft FA "DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark." BMC Bioinformatics. 2019 Oct 11;20(1):493. https://doi.org/10.1186/s12859-019-3108-7
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