Changes

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 chr$chr.imputed

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

| Mappings between marker names in earlier versions of dbSNP and the preferred marker names in the current version. The file can be downloaded from [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz here].

| Mappings between marker names in earlier versions of dbSNP and the preferred marker names in the current version. The file can be downloaded from [http://www.sph.umich.edu/csg/abecasis/downloads/dbsnp134-merges.txt.gz here].

|-  

|-  

| <code>--snps target.snps.gz </code>

| <code>--snps chr.snps </code>

| SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.

| SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.

|-  

|-  

| <code>--haps target.hap.gz </code>

| <code>--haps chr.haps.gz </code>

| Phased haplotypes where missing genotypes will be imputed.

| Phased haplotypes where missing genotypes will be imputed.

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