1,555
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMinimac: 1000 Genomes Imputation Cookbook (view source)
Revision as of 10:06, 5 August 2011
, 10:06, 5 August 2011→Further Time Savings
# Estimate haplotypes for all individuals, one chromosome at a time
# Estimate haplotypes for all individuals, one chromosome at a time
foreach chr (`seq 1 22`)
foreach chr (`seq 1 22`)
mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --sample 5 --prefix chr$chr.haps &
mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --sample 5 --prefix chr$chr.haps >& chr$chr-mach.log &
end
end
wait
wait
# Impute into phased haplotypes
# Impute into phased haplotypes
foreach chr (`seq 1 22`)
foreach chr (`seq 1 22`)
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps chr$chr.haps.gz --snps chr$chr.snps --rounds 5 --states 200 --prefix chr$chr.imputed &
minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --haps chr$chr.haps.gz --snps chr$chr.snps --rounds 5 --states 200 --prefix chr$chr.imputed >& chr$chr-minimac.log &
end
end
wait
wait
@ overlap = 500
@ overlap = 500
# Estimate haplotypes for all individuals, in 5000 marker chunks, with 500 marker overhang
# Estimate haplotypes for all individuals, in 2500 marker chunks, with 500 marker overhang
foreach chr (`seq 1 22`)
foreach chr (`seq 1 22`)
