This page summaries the SV pipelines used in GoNL == SV modules == Because of different coverage, the following software are used to call SVs from GoNL data. * Pindel: Eric-Wubbo, Kai * DWAQseq/1-2-3 SV: Victor, Slavik * Breakdancer: Jayne, Joep * GenomeSTRiP: Bob, Laurent * CNVnater: Abdel The following software are used to assemble reads to detect novel (large) insertions. * soapdenovo: Victor * Abyss: Aby == Pilot phase == 16 trios, 4 quartets are used for pilot test. Here are the software setup. ==== Pindel ==== ==== DWAQseq/1-2-3 SV ==== ==== Breakdancer ==== ==== GenomeSTRiP ==== ==== CNVnater ==== ==== soapdenovo ==== ==== Abyss ==== == Production phase == UMCG BAMs to be used for production calls. ==== Pindel ==== ==== DWAQseq/1-2-3 SV ==== ==== Breakdancer ==== ==== GenomeSTRiP ==== ==== CNVnater ==== ==== soapdenovo ==== ==== Abyss ====