We note that the use of somatic mutation allelic-fractions, combined with the SCNA copy-ratios, generally allows for increased sensitivity for samples with few SCNAs. In addition, the mutation data helps distinguish genome-doubling ambiguity in purity/ploidy estimation, although they do not inform ambiguities of the type b′ = b + 2(1-α)/D (Supplementary Fig. 1d,i, eq. 1). Thus, combined analysis generally facilitates obtaining higher call-rates using ABSOLUTE (not shown).
