SAEC exec sum

Revision as of 15:43, 18 January 2008 by Bjagla (talk | contribs) (SAEC Executive summary of data preparation)

SAEC Executive summary of data preparation

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Data reformatting

The original Illumina data that came in four comma separated files [+] where divided up by subject and stored in separate files [**]. 4 subject duplicates in Illumina records were removed based on their call rate[+].

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

WG0012277-DNA_A10_2948_A10 and WG0012277-DNA_F04_2948_F04.

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?