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\subsection{How WASP mapping works}  To use the WASP mapping pipeline, reads are first mapped using a mapping too chosen by the user. The   WASP maps reads using any mapper of the users  mapping is to remove reads   First, reads are mapped normally using a mapper chosen by the user (must output BAM or SAM format). Then mapped reads that overlap single nucleotide polymorphisms (SNPs) are identified. For each read that overlaps a SNP, its genotype is swapped with that of the other allele and the read is re-mapped. Re-mapped reads that fail to map to exactly the same location in the genome are discarded.