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Table 1 Overview of the SM callsets used in the study

From: Functional chromatin features are associated with structural mutations in cancer

Callset Number of samples Number of SM events Sequencing platform Aligner Original reference genome Caller Reference
Wellcome Trust Sanger Institute
Breast-Stephens 24 2113 Illumina GAII 2 × 37 bp insert 500 bp MAQ hg18 SSAHA [6]
Breast-NikZainal 21 1149 Illumina GAIIx 2 × 108 bp Hiseq 2000 2 × 100 bp insert <700 bp bwa/MAQ hg19 SSAHA [21]
Ovarian-McBride 13 631 Illumina GA2 2 × 37 bp insert 200-500 bp bwa hg19 SSAHA [22]
Broad Institute
Colorectal-Bass 9 653 Illumina GA-II 2 × 101 bp insert 400 bp MAQ hg18 dRanger [23]
Head&Neck-Stransky 2 126 Illumina GA II 2 × 101 bp insert 380-400 bp bwa hg19 dRanger [24]
Prostate-Berger 7 755 Illumina GA II 2 × 101 bp insert 400 bp MAQ hg18 dRanger [25]
Prostate-Baca 57 5710 Illumina GA II 2 × 101 bp insert 340 bp bwa hg19 dRanger [26]
Other
Breast-Inaki 14 3463 SOLiD long span 10 kb 2 × 36 bp Corona Lite bwa hg18 hg19 custom unnamed [27, 28]