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 |