The gentle-clipped sequences that overhang the breakpoint are collapsed right into a consensus sequence employing a various sequence alignment (MSA) delivered during the seqAn library [27]. Wham applies 3 filters to your consensus sequences. Breakpoints are certainly not noted in conditions the place consensus sequences are shorter than 10 bp or incorporate over fifty% mismatches from the alignment, because they more probable replicate mapping glitches as opposed to allelic heterogeneity. Overlapping alleles that don't share a similar breakpoints are described as unbiased documents inside the VCF file, making it possible for for allelic heterogeneity. Various alleles Together with the very same breakpoints that fail the mismatch consensus filter are discarded.
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For an in depth description of the datasets useful for the subsequent analyses and application versions begin to see the Supporting details.
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