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Alignment of short, paired-end reads to a genome may lead to a perfect match or to a partial match (e.g. a match carrying small insertions or deletions or mismatches). Although the ability of an aligner to identify suboptimal mapping is critical for single nucleotide or small indel variants identification, the presence of suboptimal matches in fusion discovery is usually detrimental, because it increases the risk of artefacts due to erroneous mapping. This is indeed another important source of artefacts in mRNAseq fusion analyses. To overcome this problem, the Cigar filter, which is activated by default, scans the alignment data for the presence of non perfect alignments. If present, these data are thus discarded.
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