snptest
Overview
| Field |
Value |
| Format key |
snptest |
| Spec file |
formats/snptest.json |
| Cite name |
SNPTEST |
| Version |
v2.5.4-beta3 |
| Source |
https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest |
| Citation |
Marchini, J., Howie, B., Myers, S., McVean, G., & Donnelly, P. (2007). A new multipoint method for genome-wide association studies via imputation of genotypes. Nature Genetics, 39(7), 906-913. |
| ## Column mapping |
|
| Raw header |
Canonical |
all_maf |
MAF |
all_total |
N |
allele_A |
NEA |
allele_B |
EA |
alleleA |
NEA |
alleleB |
EA |
alternate_ids |
SNPID |
average_maximum_posterior_call |
INFO |
bayesian_add_beta_1 |
BETA |
bayesian_add_pvalue |
P |
bayesian_add_se_1 |
SE |
cases_maf |
MAF_CASE |
cases_total |
N_CASE |
chromosome |
CHR |
controls_maf |
MAF_CONTROL |
controls_total |
N_CONTROL |
freq_allele_B |
EAF |
freq_alleleB |
EAF |
freqA |
EAF |
freqB |
EAF |
frequentist_add_beta_1 |
BETA |
frequentist_add_OR_1 |
OR |
frequentist_add_OR_95L_1 |
OR_95L |
frequentist_add_OR_95U_1 |
OR_95U |
frequentist_add_pvalue |
P |
frequentist_add_se_1 |
SE |
id |
SNPID |
info |
INFO |
pos |
POS |
position |
POS |
rsid |
rsID |
| ## Coverage |
|
9/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
yes |
EA, NEA |
— |
| Effect size |
yes |
BETA, OR |
HR, Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
yes |
N, N_CASE |
— |
| Allele frequency |
yes |
EAF, MAF |
NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
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