Improvement in detection of minor alleles in next generation sequencing by base quality recalibration. Improvement in detection of minor alleles in next generation sequencing by base quality recalibration

Minor allele detection in high coverage sequence data has many applications such as mtDNA heteroplasmy, somatic mutations in cancer or tumors, SNP calling in pool sequencing, etc. We introduce a new approach (called SEGREG) for base quality recalibration to cover such applications, and we show that this approach outperforms the currently available tools for this purpose (such as GATK and BAQ) when applied to simulated data. We further investigate sequence error and recalibration parameters by applying SEGREG-based log likelihood ration (LLR) analysis to phiX174 DNA sequenced to very high coverage, and to mtDNA genome sequences previously analyzed for heteroplasmic variants. Our results suggest that SEGREG-based LLR can identify more true minor alleles, while avoiding false positives from sequencing error, than other approaches.