Changes

We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.  

We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.  

== How do I get reference files for an region of interest? ==

== How do I get reference files for an region of interest? ==

Note that you do not need to extract regional pedigree files for your own samples because SNPs in pedigree but not in reference will be automatically discarded. <br>

Note that you do not need to extract regional pedigree files for your own samples because SNPs in pedigree but not in reference will be automatically discarded. <br> 1. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br> 2. For MACH format, you can do the following:  

1. For HapMapII format, download haplotypes from http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br>

2. For MACH format, you can do the following:  

*First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.  

*First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.  

   @ first = `grep -nw rsFIRST orig.snps | cut -f1 -d ':'`

   @ first = `grep -nw rsFIRST orig.snps | cut -f1 -d ':'`

  @ last = `grep -nw rsLAST orig.snps | cut -f1 -d ':'`

@ last = `grep -nw rsLAST orig.snps | cut -f1 -d ':'`

*Finally (assuming the third field contains the actual haplotypes, where alleles are separated by whitespace):

*Then find out the field that contains the actual haplotypes, where alleles are separated by whitespace

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

 

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

The created reference files are in MaCH format. You do NOT need to turn on --hapmapFormat option.

The created reference files are in MaCH format. You do NOT need to turn on --hapmapFormat option.