Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data

Table 2 Purity estimates by all methods

Coverage	True purity	Accucopy	Sequenza	ABSOLUTE	Sclust
2X	0.1	0.1047	1.0	0.26	–
2X	0.2	0.2069	1.0	0.21*	–
2X	0.3	0.31214	0.98	0.32*	–
2X	0.4	0.41966	0.47	0.42*	–
2X	0.5	0.5199	0.56	0.53*	0.59
2X	0.6	0.62211	0.66	0.31	0.61
2X	0.7	0.73768	0.86	0.37	0.74
2X	0.8	0.83951	0.91	0.72	0.63
2X	0.9	0.94051	0.95	0.61	0.99
5X	0.1	0.09751	0.13	0.22	–
5X	0.2	0.20108	0.22	0.2*	–
5X	0.3	0.31011	0.38	0.36	0.24
5X	0.4	0.40559	0.44	0.41*	0.32
5X	0.5	0.51208	0.55	0.69	0.37
5X	0.6	0.6125	0.65	0.47	0.64
5X	0.7	0.71576	0.76	0.36	0.72
5X	0.8	0.816	0.84	0.81*	0.81
5X	0.9	0.91884	0.94	0.46	0.98
10X	0.1	0.098563	0.29	0.22	0.27
10X	0.2	0.20085	0.31	0.25	–
10X	0.3	0.30411	0.36	0.27	–
10X	0.4	0.40553	0.42	0.51	0.3
10X	0.5	0.5066	0.52	0.51*	–
10X	0.6	0.60569	0.63	0.3	0.65
10X	0.7	0.70754	0.74	0.53	0.7
10X	0.8	0.80739	0.83	0.8*	0.83
10X	0.9	0.90612	0.94	0.45	0.92

Asterisk (*) in the ABSOLUTE column indicates ABSOLUTE performed well on the sample. Dash (–) in the Sclust column indicates Sclust failed on the sample

ISSN: 1471-2105