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43 bytes added
, 10:06, 5 August 2011
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| # 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$chr-mach.log & |
| end | | end |
| wait | | wait |
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| # Impute into phased haplotypes | | # Impute into phased haplotypes |
| foreach chr (`seq 1 22`) | | foreach chr (`seq 1 22`) |
− | minimac --refHaps ref.hap.$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 |
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| @ 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`) |
| | | |