deletions | additions       diff --git a/Testing against N masked.tex b/Testing against N masked.tex  index e97a69a..b79fbe0 100644  --- a/Testing against N masked.tex  +++ b/Testing against N masked.tex 
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We evaluated the performance of WASP compared to mapping to a perosonal or N-masked genome. To create an N-masked genome, we created a copy of the hg18 genome with Ns in place of known variants from the GM12878 cell line. We similarly created maternal and paternal copies of GM12878 using the phased genotpes from HapMap phase 2.  We mapped the simulated reads to the N-masked genome and personal genomes with BWA \cite{Li_2009}, using default parameters. \cite{Li_2009} allowing up to 2 mismatches per read (\verb|-n 2|), and excluding gapped alignments (\verb|-o 0|).