geWorkbench

= SAEC Executive summary of data preparation=
"<font color="red">[+]</font>" denotes hidden additional information. Clicking on the "<font color="red">+</font>" shows that information. "<font color="red">[*]</font>" denotes available mouse-over information.
== Data reformatting ==
The original Illumina data that came in four comma separated files <span class="toggleblock" title="csv_files">[<font>+</font><font style="display:none;">–</font>]</span> where divided up by subject and stored in separate files <span class="toggleblock" title="located on ~/SJS/Genotypes">[<font>*</font><font style="display:none;">*</font>]</span>.
4 subject duplicates in Illumina records were removed based on their call rate<span class="toggleblock" title="removed_Illumina_Subjects">[<font>+</font><font style="display:none;">–</font>]</span>.

<div id="csv_files" class="hiddenblock">
 PGx40001_12278-DNA.csv
 PGx40001_GSK_SJS_B137_28Aug2007_Genotype_Report_12276-DNA.csv
 PGx40001_GSK_SJS_B137_28Aug2007_Genotype_Report_12277-DNA.csv
 PGx40001_GSK_SJS_B137_28Aug2007_Genotype_Report_12914-DNA.csv
</div>

<div id="removed_Illumina_Subjects" class="hiddenblock">
WG0012277-DNA_A10_2948_A10 and WG0012277-DNA_F04_2948_F04.
</div>

== PLINK input data ==
info on reformatting

== removing SNPs without founder genotype ==
link to file

== Individuals removed ==
removed because (link to results) concordance + ethnic inconsistancies

== SNPs removed ==
SNPs where removed based on more than one criteria, which ones? where are the results?