SNP-calling was performed using VarScan v2.2.3 [16] on pileup files generated with SamTools v0.1.12a [6]. As we were interested in identifying low-frequency true SNPs and associated false positives (errors), the minimum variant frequency parameter was set to zero. Minimum coverage was set to 100 and the minimum number of reads supporting each SNP was set to five. As VarScan largely depends on individual base quality scores to distinguish between true SNPs and sequencing errors, we varied the minimum average quality (M.A.Q.) parameter from 10 to 40 and investigated its interaction with specific error profiles and SNP-calling accuracy.
