PT  - JOURNAL ARTICLE
AU  - Daniel L Cameron
AU  - Jan Schroeder
AU  - Jocelyn Sietsma Penington
AU  - Hongdo Do
AU  - Ramyar Molania
AU  - Alexander Dobrovic
AU  - Terence P Speed
AU  - Anthony T Papenfuss
TI  - GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly
AID  - 10.1101/110387
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 110387
4099  - http://biorxiv.org/content/early/2017/02/21/110387.short
4100  - http://biorxiv.org/content/early/2017/02/21/110387.full
AB  - The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massively parallel sequencing remains a major challenge. Here, we describe the Genome Rearrangement IDentification Software Suite (GRIDSS), a high-speed structural variant (SV) caller that performs efficient genome-wide break-end assembly prior to variant calling using a novel positional de Bruijn graph 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 tumour data, recently winning SV sub-challenge #5 of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge. On human cell line data, GRIDSS halves the false discovery rate compared to other recent methods. GRIDSS identifies non-template sequence insertions, micro-homologies and large imperfect homologies, and supports multi-sample analysis. GRIDSS is freely available at https://github.com/PapenfussLab/gridss.