Literature

Abyzov-2011

Abyzov,A. et al. (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res., 21, 974--984.

Abyzov-2015

Abyzov,A. et al. (2015) Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms. Nat. Commun., 6, 7256.

Chen-2009

Chen,K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677--681.

Chen-2016

Chen,X. et al. (2016) Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32, 1220--1222.

Chiu-2021

Chiu,R. et al. (2021) Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol., 22, 224.

Haas-2017

Haas,B et al. (2017) STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. doi: https://doi.org/10.1101/120295

Iyer-2011

Iyer,M.K. et al. (2011) ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics, 27, 2903--2904.

MacDonald-2014

MacDonald,J.R. et al. (2014) The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res., 42, D986--92.

McPherson-2011

McPherson,A. et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol., 7, e1001138.

Rausch-2012

Rausch,T. et al. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics, 28, i333--i339.

Robertson-2010

Robertson,G. et al. (2010) De novo assembly and analysis of RNA-seq data. Nat. Methods, 7, 909--912.

Saunders-2012

Saunders,C.T. et al. (2012) Strelka: accurate somatic small-variant calling from sequenced tumor--normal sample pairs. Bioinformatics, 28, 1811--1817.

Uhrig-2021

Uhrig,S. et al. (2021) Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Res., 31, 448--460.

Yates-2016

Yates,A. et al. (2016) Ensembl 2016. Nucleic Acids Res., 44, D710--D716.

Ye-2009

Ye,K. et al. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865--2871.

den-Dunnen-2016

den Dunnen,J.T. et al. (2016) HGVS Recommendations for the Description of Sequence Variants: 2016 Update. Hum. Mutat., 37, 564--569.