ResultsSharingFormat

The following variables should be included when sharing imputed results for meta-analysis; large files can be shared among small groups via secure file transfer site (as described in Results Sharing)

variable name	description
SNPID	SNP ID as rs number
chr	chromosome number. Use symbols X, XY, Y and mt for non-autosomal markers.
position	physical position for the reference sequence (build 35 strongly preferred)
coded_all	coded allele, also called modeled allele (in example of A/G SNP in which AA=0, AG=1 and GG=2, the coded allele is G)
noncoded_all	the alternate allele
strand_genome	+ or -, representing either the positive/forward strand or the negative/reverse strand of the human genome reference sequence; to clarify which strand the coded_all and noncoded_all are on
beta	beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available
SE	standard error of beta estimate, to at least 5 decimal places -- “NA” if not available
pval	p-value of test statistic, here just as a double check -- “NA” if not available
AF_coded_all	allele frequency for the coded allele -- “NA” if not available
HWE_pval	exact test Hardy-Weinberg equilibrium p-value -- only directly typed SNPs, NA for imputed
callrate	genotyping callrate after exclusions
n_total	total sample with phenotype and genotype for SNP
imputed	1/0 coding; 1=imputed SNP, 0=if directly typed
used_for_imp	1/0 coding; 1=used for imputation, 0=not used for imputation
oevar_imp	observed divided by expected variance for imputed allele dosage -- NA otherwise
avpostprob	average posterior probability for imputed SNP allele dosage* (applies to best-guess genotype imputation)

Please note that a README should be uploaded with a very brief description of the data uploaded, the date, the NCBI human genome reference sequence used (e.g. NCBI 36.2) for strand reference, and the scale of the beta estimates; please also include in the README the SNP HWE p-value, callrate and minor allele frequency filters that have been applied.