Changes

  # step 2:

  # step 2:

  mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log

  mach1 -d sample.dat -p sample.ped -s chr20.snps -h chr20.hap --compact --greedy --autoFlip --errorMap par_infer.erate --crossoverMap par_infer.rec --mle --mldetails > mach.imp.log

=== '''Where can I find combined HapMap reference files? '''  ===

=== '''Where can I find combined HapMap reference files? '''  ===

Yes, but not often. The --mle option outputs the most likely genotype configuration taking into account observed genotypes and integration over the most similar reference haplotypes. The original genotypes will be changed only if the underlying reference haplotypes strongly contradict the input genotype.  

Yes, but not often. The --mle option outputs the most likely genotype configuration taking into account observed genotypes and integration over the most similar reference haplotypes. The original genotypes will be changed only if the underlying reference haplotypes strongly contradict the input genotype.  

 

=== How do I get imputation quality estimates?  ===

=== How do I get imputation quality estimates?  ===

If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, you will probably avoid problems by including markers in the pedigree file sorted in chromosome order.  

If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, you will probably avoid problems by including markers in the pedigree file sorted in chromosome order.  

 

=== '''What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''  ===

=== '''What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''  ===

Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs.  

Based on the three files above, we've confirmed that dosage is the number of AL1 copies: you will only to check for one informative case (i.e, dosage values close to 0 or 2) since it's consistent across all individuals and all SNPs.  

 

=== '''Can I used unphased reference?'''  ===

=== '''Can I used unphased reference?'''  ===

Equivalently, you could write -d reference.dat,sample.dat -p reference.ped,sample.ped on the command line and MACH would merge both files ''on-the-fly''.  

Equivalently, you could write -d reference.dat,sample.dat -p reference.ped,sample.ped on the command line and MACH would merge both files ''on-the-fly''.  

 

=== '''How long does imputation take?'''  ===

=== '''How long does imputation take?'''  ===