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Test EPACTS for DIAGRAM (view source)

Revision as of 14:59, 4 October 2012

593 bytes added ,  14:59, 4 October 2012
→‎Expected output
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The columns in the results file are:
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#CHROM: &nbsp;chromosome
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#BEGIN: &nbsp;starting position
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#END: ending position (same as BEGIN if a SNP)
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#MARKER_ID: &nbsp;name of varian
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#NS: &nbsp;Number of samples (cases + controls)
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#AC: &nbsp;Total allele count in sample
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#CALLRATE: &nbsp;call rate
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#MAF: &nbsp;minor allele frequency in full sample
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#PVALUE: &nbsp;score test association p-value
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#SCORE: &nbsp;test statistic for score test
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#N.CASE: &nbsp;number of cases
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#N.CTRL: &nbsp;number of controls
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#AF.CASE: &nbsp;allele frequency in cases only
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#AF.CTRL: &nbsp;allele frequency in controls only
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Note: &nbsp;For variants below the minimum MAF threshold (min-maf = 0.001), the number of cases and controls (N.CASE, N.CTRL) are not outputted (listed as "NA").  
 
Note: &nbsp;For variants below the minimum MAF threshold (min-maf = 0.001), the number of cases and controls (N.CASE, N.CTRL) are not outputted (listed as "NA").  
  
Clement Ma
216

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