Functional chromatin features are associated with structural mutations in cancer

BMC Genomics

Table 1 Overview of the SM callsets used in the study

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]

ISSN: 1471-2164