Changes

A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout:  

A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout:  

Comparing 948352 masked genotypes with MLE estimates ...<br> Estimated per genotype error rate is 0.0568<br> Estimated per allele error rate is 0.0293<br><br>

  Comparing 948352 masked genotypes with MLE estimates ...<br> Estimated per genotype error rate is 0.0568<br> Estimated per allele error rate is 0.0293<br><br>  

<br>  

<br>  

   awk '{print $3}' orig.hap | cut -c${first}-${last} &gt; region.hap

   awk '{print $3}' orig.hap | cut -c${first}-${last} &gt; region.hap

<br>'''Q: Do I have to sort the pedigree file by physical positions? '''<br> A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br>

<br>'''Q: Do I have to sort the pedigree file by physical positions? '''<br> A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br>  

<br>'''Q: What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''<br> A: mach automatically resets it to maximum possible value.  

<br>'''Q: What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''<br> A: mach automatically resets it to maximum possible value.  

<br>

<br>  

'''Q: Can I used unphased reference?'''<br>  

'''Q: Can I used unphased reference?'''<br>