1000G 2009-08 Download
Original data (generated by Yun Li, Goncalo Abecasis and colleagues) are the August 2009 release of phased data from the 1000 Genomes Project,
downloadable from ftp://share.sph.umich.edu/1000genomes/pilot1/. Two
individuals (the father and daughter of the trio in Pilot 2 [namely, NA12891 and NA12878])
were removed because no sequencing data were used to built the haplotypes,
resulting in 122 haplotypes.
Singletons (SNPs with minor allele appearing once) are removed.
The files can be directly fed to mach. We recommend a 2-step imputation procedure:
(step 1) a representative subset of >= 200 unrelated individuals are used to calibrate model parameters; and
(step 2) actual genotype imputation is
performed for every person using parameters inferred in step 1.
Example command lines for a 2-step imputation:
mach1 -d sample.dat -p subset.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip -r 100 -o par_infer > mach.infer.log
mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle
--mldetails > mach.imp.log
Report to Yun Li if a large number of genotyped SNPs are discarded due to absence in this
reference. You can check through the following command line
> grep "will be ignored" mach.*.log
Do not turn on --compact if memory is not an issue.