Lossy CRAMs for mapped phase3 BAMs are available now on the ftp site:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data
In these lossy crams, the quality scores were binned according to Illumina 8-binning scheme; tags OQ, BQ, CQ were dropped.
Two index files for the lossy CRAMs can be found in
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices with the following names:
20130502.alignment.lossy_cram.index
20130502.exome.alignment.lossy_cram.index
The average size of the lossy crams is 30.7% and 31.0% of that of the low coverage and exome BAMs, respectively.
The above information can also be found in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/README.crams