Table 1.

Features of peak calling methods

	GEM	BCP (TF)	BCP (Histone)	MUSIC	MACS2	ZINBA	TM
Locating the potential peaks
High resolution	Yes	Yes	No	Yes	Yes	No	Yes
ChIP and input sample signals combined	No	No	No	No	No	Yes	Yes
Multiple alternate window sizes	Yes	Yes	Yes	Yes	No	No	No
Use of variability of local signal	Yes	Yes	Yes	No	Yes	Yes	No
Ranking of peaks
Binomial test	Yes	No	No	Yes	No	No	No
Poisson test	No	Yes	No	No	Yes	No	No
Normalized difference score	No	No	No	No	No	No	Yes
Use of underlying genome sequence	Yes	No	No	No	No	No	No
Posterior probability of enrichment	No	No	Yes	No	No	Yes	No

Note. See Supplementary Table S1 for a more complete list of features and peak calling methods.