I'm working on imputing GWAS data to the 1000 Genomes Project data using MaCH. For the model estimation phase you only need ~200 individuals. Here's a one-line unix command that will pull out 200 samples at random from a binary pedigree .fam file called myfamfile.fam: for i in `cut -d ' ' -f 1-2  myfamfile.fam | sed s/\ /,/g`; do echo "$RANDOM $i"; done | sort |

As I mentioned in my recap of the ASHG 1000 genomes tutorial, I'm doing to be imputing some of my own data to 1000 genomes, and I'll try to post lessons learned along the way here under the 1000 genomes and imputation tags. I'm starting from a binary pedigree format file (plink's bed/bim/fam format) and the first thing in the 1000 genomes imputation cookbook is to store your data in Merlin format, one per chromosome.