This page summaries the SV pipelines used in GoNL == SV tasks == Because of different coverage, the following software are used to call SVs from GoNL data. * Pindel: Eric-Wubbo, Kai * DWAC-seq/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 PCR/chip validation is performed by Wigard, Johan. == Pilot phase (Sep, Oct 2011) == 16 trios, 4 quartets are used for pilot test. Refer to the sample file for detailed sample IDs. ==== Pindel ==== * used command line * result location ==== DWAC-seq/1-2-3 SV ==== ==== Breakdancer ==== ==== GenomeSTRiP ==== ==== CNVnater ==== ==== soapdenovo ==== ==== Abyss ==== == Validation (Oct 2011) == TBA == Production phase (Nov, Dec 2011)== UMCG BAMs to be used for production calls. ==== Pindel ==== * used command line ==== DWAC-seq/1-2-3 SV ==== ==== Breakdancer ==== ==== GenomeSTRiP ==== ==== CNVnater ==== ==== soapdenovo ==== ==== Abyss ====