The soft-clipped sequences that overhang the breakpoint are collapsed into a consensus sequence using a a number of sequence alignment (MSA) delivered inside the seqAn library [27]. Wham applies a few filters towards the consensus sequences. Breakpoints aren't noted in conditions where by consensus sequences are shorter than ten bp or comprise more than fifty% mismatches from the alignment, as they a lot more most likely replicate mapping problems rather then allelic heterogeneity. Overlapping alleles that do not share exactly the same breakpoints are documented as independent information from the VCF file, making it possible for for allelic heterogeneity. Unique alleles Using the identical breakpoints that fall short the mismatch consensus filter are discarded.
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