Mucaki et al published an article in BMC Medical Genomics entitled “A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer”.

Their pipeline uses both CRAC and Casava for the sequence alignment, then SNVs and indels were called using GATK. There is little agreement between both methods and the authors exhibit an example of a discordance, which is at CRAC’s advantage.

Mucaki et al's example