The alignments based on the 20100611.sequence.index have been released. There are both new BAM files and updated BAM files with more data were added. For the case of updated files, the older, redundant files have been withdrawn.
Illumina data was aligned at the Sanger Institute and SOLiD data at TGEN. More information is available in the README file linked below. Full project data is aligned to the GRCh37 human assembly.