deletions | additions       diff --git a/Genotyping and Filtering.tex b/Genotyping and Filtering.tex  index d4722df..55b7911 100644  --- a/Genotyping and Filtering.tex  +++ b/Genotyping and Filtering.tex 
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generated SNP set, and not used for any part of the SNP discovery  procedures.  An alternative approach to genotyping a group of individuals from a  target group is to use large public (and free) datasets from the  closest matching groups to generate the initial set. This approach  would be used if large-scale genotyping from the target group were  unavailable, or would be prohibitively expensive.  While genotyping similar groups is much cheaper, it also has a high  chance of misses for relevant markers, as the marker mutation profile  of populations can differ quite significantly between populations. As  a demonstration of this, allele frequency differences between HapMap  CEU and HapMap CHB populations were calculated for SNPs in a 10Mb  region centred on the ADH region. In this case, the HapMap CHB  population was used as a proxy for the Maori population. A total of 37  SNPs were selected, all with allele frequency differences greater than  0.5, for then genotyping in 45 Maori (the target group). Of these 37  SNPs, 19 had allele frequency differences between HapMap CEU and Maori  populations of less than 0.2, and only 2 SNPs had allele frequency  differences greater than 0.5.  \subsubsection{Marker Association Values Across the Entire Genome}  \label{sec:meth-summ-genotyping-ranking} 
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$5^\prime$ end of the reference strand).