The official release of phase2 alignment data is complete and available on the ftp site. All BAMs have gone through the DCC QA process; samples and runs identified as problematic have been withdrawn. The 20111114.sequence.index has been updated to reflect the withdrawn.
The alignment index files are:
Low Coverage data (Illumina, 454 and SOLiD)
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices/20111114.alignment.index or
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment.index
EXOME data (Illumina and SOLiD)
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices/20111114.exome.alignment.index or
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/exome.alignment.index
In the alignment_indices directory ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/alignment_indices/, you may find associated stats files and summary bas files:
Low Coverage:
20111114_20101123.alignment_stats.low_coverage.csv
20111114.alignment.index.bas.gz
EXOME:
20111114_20101123.alignment_stats.exome.csv
20111114.exome.alignment.index.bas.gz
20111114.exome.alignment.index.HsMetrics.gz
20111114.exome.alignment.index.HsMetrics.stats