Wham is designed for paired-end Illumina libraries with normal insert measurements (~300bp-500bp). Wham integrates mate-pair mapping, break up go through mapping, smooth-clipping, alternative alignment and consensus sequence based mostly evidence to predict SV breakpoints with single-nucleotide accuracy. Wham generates a mixed pileup (catalog of reads covering a posture of the genome) for all BAM documents delivered. Reads from all men and women included in joint contacting that are soft or really hard clipped are hashed by posture to detect shared breakpoints. Positions in the pileup where by a few or even more Principal reads share the exact same breakpoint are interrogated for a putative SV.
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, as Wham conducts genotyping and Affiliation testing independent in the SV variety. Right here we explore the accuracy of Wham’s SV detection and genotyping, to start with by utilizing simulated small-examine datasets, followed by two full genome human datasets. We also use Wham to identify biologically significant structural variants in non-human data.