RT Journal
A1 Cameron, Daniel L.
A1 Schröder, Jan
A1 Penington, Jocelyn Sietsma
A1 Do, Hongdo
A1 Molania, Ramyar
A1 Dobrovic, Alexander
A1 Speed, Terence P.
A1 Papenfuss, Anthony T.
T1 GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
JF Genome Research 
JO Genome Research 
YR 2017 
FD December 01 
VO 27 
IS 12 
SP 2050 
OP 2060 
DO 10.1101/gr.222109.117 
UL http://genome.cshlp.org/content/27/12/2050.abstract 
AB The identification of genomic rearrangements with high sensitivity and specificity using massively parallel sequencing remains a major challenge, particularly in precision medicine and cancer research. Here, we describe a new method for detecting rearrangements, GRIDSS (Genome Rearrangement IDentification Software Suite). GRIDSS is a multithreaded structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph-based assembler. By combining assembly, split read, and read pair evidence using a probabilistic scoring, GRIDSS achieves high sensitivity and specificity on simulated, cell line, and patient tumor data, recently winning SV subchallenge #5 of the ICGC-TCGA DREAM8.5 Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods while matching or exceeding their sensitivity. GRIDSS identifies nontemplate sequence insertions, microhomologies, and large imperfect homologies, estimates a quality score for each breakpoint, stratifies calls into high or low confidence, and supports multisample analysis.