ChunkChromosome

ChunkChromosome is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices.

Parameters

ChunkChromosome expects three parameters:

• A data file (specified with the -d command line option), listing all the markers along one chromosome. The data file can optionally include phenotype and other information, which is safely ignored.
• A desired core chunk size, in markers (specified with the -n command line option and defaulting to 5000 markers).
• A desired overlap between chunks, also in markers (specified with the -o command line option and defaulting to 500 markers).

Usage

Suppose you plan to run 1000 Genomes Imputation using MaCH and minimac. Typically, you'd accomplish this by running the two commands:

mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr1
minimac --refHaps 1000genomes.chr1.hap.gz  --refSnps 1000genomes.chr1.snps --haps chr1.hap.gz --snps chr1.snps  --rounds 5 --states 200 --prefix imputation-results