The tender-clipped sequences that overhang the breakpoint are collapsed right into a consensus sequence employing a several sequence alignment (MSA) supplied inside the seqAn library [27]. Wham applies 3 filters for the consensus sequences. Breakpoints will not be noted in circumstances the place consensus sequences are shorter than ten bp or consist of greater than 50% mismatches inside the alignment, because they far more likely mirror mapping problems rather then allelic heterogeneity. Overlapping alleles that don't share a similar breakpoints are noted as impartial records during the VCF file, allowing for allelic heterogeneity. Different alleles Using the exact same breakpoints that fall short the mismatch consensus filter are discarded.
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