Fig. 3

Bcftools excludes indels reported in input alignment results. a Illustration of two examples where bcftools excludes an insertion (Example 1) and reports a FP deletion (Example 2). A “-” represents a deletion. b The inner distance between paired-end reads influences the recognition of insertion by bcftools but not by QuickVariants. The inner distance of paired-end reads was computed as the distance between the alignment position of the end of read 1 and start of read 2. If two reads aligned to different contigs, the distance was computed as the closest distance between these positions in theory. c Indel identification in sample AkMu with a 4e-2 mutational density. The impact of the criterion for indel frequency on the accuracy of indel identification. The blue line represents the indel frequency threshold selected in this study