How are your alignments generated?
The 1000 genomes alignments are produced using 3 different algoriths, BWA for the Illumina runs, ssaha for the 454 runs and BFAST for the SOLiD runs. The full process is describe in the README
The 1000 genomes alignments are produced using 3 different algoriths, BWA for the Illumina runs, ssaha for the 454 runs and BFAST for the SOLiD runs. The full process is describe in the README