The comfortable-clipped sequences that overhang the breakpoint are collapsed into a consensus sequence employing a a number of sequence alignment (MSA) delivered inside the seqAn library [27]. Wham applies three filters to the consensus sequences. Breakpoints are certainly not claimed in situations wherever consensus sequences are shorter than 10 bp or incorporate greater than fifty% mismatches within the alignment, since they far more very likely mirror mapping problems in lieu of allelic heterogeneity. Overlapping alleles that do not share precisely the same breakpoints are documented as independent data during the VCF file, permitting for allelic heterogeneity. Distinct alleles Along with the identical breakpoints that fail the mismatch consensus filter are discarded.

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