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To the Editor: Traditional strategies for identification of causal mutations involve two discrete steps: recombinant genotyping and candidate gene sequencing. To dramatically speed up identification of causative point mutations and small deletions, we provide the software package SHOREmap (http://1001genomes.org/downloads/shore.html), an extension of the short read analysis pipeline SHORE1. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants, as recently proposed2.
