We are hoping to use 1000 Genomes samples as a population control for our study. The 1000 Genomes Project provides fastq, BAM and VCF files on their ftp site. We do not want to use VCF files as they have been filtered and might not contain variants occurring in our samples (especially false-positive variants in our samples). Using dbSNP is problematic for the same reason.

So it seems like a good alternative is to use 1000 Genomes BAM files. However, it would save us compute time if we could use gVCF files. Does anyone know if gVCF files from 1000 Genomes Project samples are publicly available?
A few years later, gVCF files from the 1000 Genomes project are now publicly available on [Figshare][1]


  [1]: https://figshare.com/collections/1000_Genomes_gVCFs/4414307/3