ResultsSharingFormat
Results Sharing
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). Many working groups use Google Drive, a secure web-based file-sharing system in partnership with by the University of Washington's computing group. The service has ample storage space for large files and limits access to a select group identified by Google Account IDs.
ShareSpace Access is arranged via working groups. New members who expect to need access to these sites should create a Google Account ID: create a new Google Account.
File Formats
Results should be shared as plain text files, with the following variable names:
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 (indicate build 35/36 in readme file) |
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 other 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 |
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.
For gene-environment interaction analyses, the following variables should be included:
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 (indicate build 35/36 in readme file) |
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 other 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 additive interaction term, 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 interaction test statistic, here just as a double check -- “NA” if not available |
df.t | degrees of freedom estimate for t reference distribution for interaction term -- “NA” if not available |
pval.t | p-value of interaction test statistic, using t reference distribution, here just as a double check -- “NA” if not available |
beta.main | beta estimate from genotype-phenotype association, at least 5 decimal places -- “NA” if not available |
SE.main | standard error of beta.main estimate, to at least 5 decimal places -- “NA” if not available |
pval.main | p-value of main test statistic, here just as a double check -- “NA” if not available |
covar.main.inter | covariance between beta and beta.main, to at least 5 decimal places -- “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 |
n_exposed | (DICHOTOMOUS EXPOSURE ONLY) number in sample exposed to environmental variable of interest [in longitudinal data, estimated number of independent observations that are exposed] |
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 |
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.