For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. The variant calling tool, Q-cpileup, exploits the Qs of nucleotides in a filtering strategy to increase specificity and is imbedded VirVarSeq, which allows variant calling starting from fastq files.
Verbist, Bie M. P.; Thys, Kim; Reumers, Joke; Wetzels, Yves; Van der Borght, Koen; Talloen, Willem; Aerssens, Jeroen; Clement, Lieven; Thas, Olivier.
VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.
BIOINFORMATICS, 31 (1):94-101; 10.1093/bioinformatics/btu587 JAN 1 2015