Wham is suitable for paired-end Illumina libraries with typical insert sizes (~300bp-500bp). Wham integrates mate-pair mapping, break up go through mapping, gentle-clipping, substitute alignment and consensus sequence dependent evidence to forecast SV breakpoints with single-nucleotide accuracy. Wham generates a merged pileup (catalog of reads mask
Wham clusters all the candidate breakpoints and rounds their positions to the nearest tenth base pair. The placement with the best read through guidance is reported. Should the gentle-clipped consensus sequence is often aligned towards the putative breakpoint region using the Smith-Waterman algorithm, the breakpoint is even more refined to The situ
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