Randomly Select Subsets of Individuals from a Binary Pedigree .fam File

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 |  cut -d' ' -f 2| sed s/,/\ /g | head -n 200

Redirect this output to a file, and then run PLINK using the --keep option with this new file.

Split up a GWAS dataset (PED/BED) by Chromosome

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. Surprisingly there is no option in PLINK to split up a dataset into separate files by chromosome, so I wrote a Perl script to do it myself. The script takes two arguments: 1. the base filename of the binary pedfile (if your files are data.bed, data.bim, data.fam, the base filename will be "data" without the quotes); 2. a base filename for the output files to be split up by chromosome. You'll need PLINK installed for this to work, and I've only tested this on a Unix machine. You can copy the source code below: