ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data

BMC Bioinformatics

Table 1 Somatic FLT3-ITD detection in TCGA data

TCGA ID	WES Avg Cov	Read length	TCGA^a ITD (length)	ITD Asm (length)	ITD Asm (Mut af)	Pindel^b (length)	Pindel (Mut af)	Genomon^c (length)
2853	182.3	100	18	18	0.011
2840	124.1	100	18	18	0.011
2877	225.2	75	18	18	0.232			18
2880	180.4	75	21	21	0.254			21
2918	76.5	75	21	21	0.113			21
2942	212.7	75	24	24	0.159			24
2875	229.9	75	30	30	0.187			30
2836	217.7	75	33	33	0.054
2879	186.9	75	33	33	0.355			33
2922	172.8	75	33	33	0.262			33
2925	141.5	75	42	42	0.291	42	0.024	42
2930	142.1	100	42					42
2895	151.4	75	45	45	0.201	45	0.059	45
2812	206.3	75	51	51	0.412	51	0.109
2869	198.8	100	54	54	0.017			54
2830	267.7	75	69	69	0.038	56	0.025	42
2921	119.3	100	24					24
2871	210.2	75	63
2913	100.5	75	66			66	0.085	66
2931	71.1	75	75			70	0.316
2844	223.5	75	87			87	0.156
2825	98.2	100	102			102	0.023
2809	113.6	100		30	0.019
2949	174.1	75		39	0.021
2915	75.2	75		51	0.058	49	0.024	51
2895	151.4	75		51	0.228	50	0.051
2934	149.9	75		57	0.058	56	0.071	57
2823	212.0	75		57	0.137	57	0.062
2833	206.1	75		75	0.004
2862	207.8	75				69	0.200	69
2923	197.1	75				74	0.025	74
2918	76.48	75				88	0.097	88
2919	189.8	75				93	0.022	93
2959	164.9	75				118	0.049
2896	146.6	75				153	0.084	153
2921	119.3	100						57
Total			22	22		18		22

All lengths are in base pairs
^areference 1, TCGA AML marker paper used as reference set for algorithmic discovery
^breference 23, Ye et al. [18]
^creference 24, Chiba et al. [17]

ISSN: 1471-2105