The official release of phase3 low coverage and exome data is completed and available on the ftp site. The alignment data were generated by Sanger Center. All BAMs have gone through the DCC QA process; samples and runs identified as problematic have been withdrawn. The 20130502.analysis.sequence.index has been updated to reflect the withdrawn:
Here are the main alignment index files:
There are 2535 samples in the index files; all of them passed QA and have both exome and low coverage data.
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 and an exome HsMetrics file:
A handful samples passed all QA but only have either low coverage data (23) or exome data (16); we keep the BAM files for these samples at
Two alignment index files can be found in the same directory: