A workflow for using SpeedSeq to align and call SVs from WGS data. A simple guide to SpeedSeq to get SNV, SVs, and to generate normal, discordant, and splitter BAM files. SNV calling with Freebayes, SV calling with LUMPY DELLY is included.
See speedseq_pipeline file for details. Additional information on SpeedSeq is available from the Hall lab at: https://github.com/hall-lab/speedseq and https://www.nature.com/articles/nmeth.3505
Image reproduced from: https://www.nature.com/articles/nmeth.3505