For many of the HapMap CEU cell lines there is low coverage genotypes available since the pilot of the 1000 genomes. Though still in most cases people would prefer to use the well studied and high confidence tag-SNPs from HapMap instead of these new 1000 genomes SNPs.
What are the main reasons for doing so? I can understand computational time is a reason and also genotype quality is a reason I could think off. What should men expect when using the 1000 genomes SNPs instead of the HapMap SNPs? And what are the caveats that people should consider before doing this? Are there any additional steps required to be taken in terms of increasing the confidence of the given genotypes?
I'm not planning on doing anything like this myself but I would like to read about this a bit more. So any general comments of pointers to must-read papers about this are highly appreciated!