The alignments of each dataset against Pinot Noir is available for download in BAM format. Links to downloadable files are listed at the end of this post.
The alignment step is a pivotal one in most genomics project, as it has to be set up and fine tuned accordingly with the goal of the project itself. Choosing relaxed or stringent parameters, for instance, greatly influence the final outcome of the alignment. Moreover, choosing to report only unique alignment or how to handle multiple mapping reads has a major role in downstream analysis.
In resequencing projects we should recall that ambiguosly mapped reads (e.g. because of duplicated regions) cannot be assigned to a precise position of the genome.