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 --prefix chr$chr.haps

./mach1 -d sample.dat -p sample.ped --rounds 20 --states 50 --phase --interim 5 --sample 5 --prefix sample.pp | tee mach.log

 

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 [http://www.sph.umich.edu/csg/abecasis/MaCH/ 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 [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH website]):

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=== Imputation into Phased Haplotypes - minimac ===

=== Imputation into Phased Haplotypes - minimac ===

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:

  == using a VCF reference panel ==

  ./minimac --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac.log

minimac --vcfReference --refHaps ref.vcf.gz --haps target.hap.gz --snps target.snps.gz --rounds 5 --states 200 --prefix results

Note: GWAS SNPs (file --snps target.snps.gz) are by default expected to be in the chr:pos format e.g. 1:1000 and on build37/hg19;

 

   

   

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:

| Optionally, a string that is used to help generate output file names.

| Optionally, a string that is used to help generate output file names.

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You can speed-up things by running minimac in parallel by launching the [http://genome.sph.umich.edu/wiki/Minimac#Multiprocessor_Version minimac-omp] version. On our cluster 4 cpus per minimac is optimal (--cpus 4).

You can speed-up things by running minimac in parallel by launching the [http://genome.sph.umich.edu/wiki/Minimac#Multiprocessor_Version minimac-omp] version. On our cluster 4 cpus per minimac is optimal (--cpus 4).

./minimac-omp --cpus 4 --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac-omp.log

 

    runon -m 1024 minimac-omp --cpus 4 --refHaps ref.hap.$chr.gz  --vcfReference  \

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