The 1000 genomes snp calling process is still evolving. The pilot analysis is described in the Nature paper A map of human genome variation from population-scale sequencing. By using low coverage data from many individuals we have show you are able to accurately predict variation shared across those individuals who are sequenced to a depth of between 3 and 5x and that you can find SNPs with minor allele frequencies of 1% and lower. The total depth of coverage used to call a particular snp is generally quoted in the info column of a given vcf file with the tag DP.

Our main variant calling strategy combines variant calls from multiple different calling algorithms which also increases the power of the analysis.

We get the ancestral alleles for our variants from Ensembl compara and are based on a 6 way primate alignment which is described in a README