Changes

A convenient way to haplotype your sample is to use MaCH. A typical MaCH command line to estimate phased haplotypes might look like this:

A convenient way to haplotype your sample is to use MaCH. A typical MaCH command line to estimate phased haplotypes might look like this:

   mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5

   mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr$chr.haps

This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 200 haplotypes. A summary description of these parameters follows (but for a more complete description, you should go to the MaCH website):

This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 200 haplotypes. A summary description of these parameters follows (but for a more complete description, you should go to the MaCH website):

   foreach chr (`seq 1 22`)

   foreach chr (`seq 1 22`)

     runon -m 4096 mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --interim 5 --sample 5

     runon -m 4096 mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr$chr.haps

   end

   end

A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:

A typical minimac command line, where the string $chr should be replaced with an appropriate chromosome number, might look like this:

   minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix results$chr

   minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix chr$chr.imputed

A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:

A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:

     runon -m 1024 minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz \

     runon -m 1024 minimac --refHaps ref.hap.$chr.gz --refSnps ref.snps.$chr.gz --snpAliases dbsnp134-merges.txt.gz \

                           --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix results$chr

                           --haps target.hap.$chr.gz --snps target.snps.$chr.gz --prefix chr$chr.imputed

   end

   end