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Table 1 Example of alignment of allelic effects and error trapping for a single SNP in a meta-analysis of five studies of a dichotomous phenotype.

From: GWAMA: software for genome-wide association meta-analysis

Study Reported strand Effect allele1 Other allele RAF Odds ratio
(95% confidence interval)
Aligned allelic effect
(standard error)
Comment
1 + A G 0.12 1.12 (1.07-1.16) 0.11 (0.02) Allele A taken as reference effect allele.
2 + G A 0.85 0.92 (0.87-0.98) 0.08 (0.03) Effect aligned to allele A.
3 - T C 0.12 1.06 (1.02-1.10) 0.06 (0.02) Effect aligned to allele A on + strand.
4 + T C 0.13 1.07 (0.99-1.16) 0.07 (0.04) Effect aligned to allele A on + strand. Strand error reported to log file.
5 + A G 0.87 0.95 (0.90-1.01) -0.05 (0.03) Large discrepancy in EAF reported to log file.
  1. 1 Effects are aligned to the reference allele in the first study. Errors in the reported strand are recorded in the log file together with warnings regarding potential discrepancies in reported data between studies, for example the aligned reference allele frequency (RAF).