auto_raw
Shared raw→canonical aliases for all auto* presets (no allele or ambiguous-frequency assumptions). Merged by scripts/sync_auto_from_raw.py; not sufficient alone for summary-stat allele harmonization.
Overview
| Field |
Value |
| Format key |
auto_raw |
| Spec file |
formats/auto_raw.json |
| Version |
20250827 |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| NA value |
#NA |
| ## Column mapping |
|
| Raw header |
Canonical |
#CHROM |
CHR |
A1_CASE_FREQ |
EAF_CASE |
A1_CTRL_FREQ |
EAF_CONTROL |
A1_FREQ |
EAF |
allelefrequency_effect |
EAF |
B |
BETA |
b |
BETA |
base_pair_location |
POS |
beta |
BETA |
BETA |
BETA |
Beta |
BETA |
BETA_95L |
BETA_95L |
BETA_95U |
BETA_95U |
betase |
SE |
BP |
POS |
bp |
POS |
bpos |
POS |
chisq |
CHISQ |
chisq_association |
CHISQ |
CHISQ_BOLT_LMM |
CHISQ |
CHR |
CHR |
chr |
CHR |
Chr |
CHR |
CHROM |
CHR |
Chrom |
CHR |
chrom |
CHR |
chromosome |
CHR |
Chromosome |
CHR |
CHROMOSOME |
CHR |
ci_lower |
OR_95L |
ci_upper |
OR_95U |
Direction |
DIRECTION |
DIRECTION |
DIRECTION |
EA |
EA |
ea |
EA |
eaf |
EAF |
EAF |
EAF |
Effect |
BETA |
effect_allele |
EA |
effect_allele_frequency |
EAF |
effect_weight |
BETA |
est |
BETA |
F |
F |
F_STAT |
F |
GENPOS |
POS |
hazard_ratio |
HR |
hm_rsID |
rsID |
HR_95L |
HR_95L |
HR_95U |
HR_95U |
I2 |
I2 |
imputationInfo |
INFO |
info |
INFO |
INFO |
INFO |
L95 |
BETA_95L |
LOG10_P |
MLOG10P |
LOG10P |
MLOG10P |
MAC |
MA_COUNT |
mac |
MA_COUNT |
MACH_R2 |
INFO |
maf |
MAF |
Maf |
MAF |
MAF |
MAF |
MAF_CASE |
MAF_CASE |
maf_case |
MAF_CASE |
MAF_CONTROL |
MAF_CONTROL |
maf_control |
MAF_CONTROL |
MARKER |
SNPID |
marker |
SNPID |
MARKERNAME |
SNPID |
markername |
SNPID |
MLOG10P |
MLOG10P |
n |
N |
N |
N |
N_CASE |
N_CASE |
n_case |
N_CASE |
N_control |
N_CONTROL |
N_Control |
N_CONTROL |
N_EFF |
N_EFF |
Ncase |
N_CASE |
ncase |
N_CASE |
Ncontrol |
N_CONTROL |
NCONTROL |
N_CONTROL |
NEA |
NEA |
nea |
NEA |
Neff |
N_EFF |
neg_log_10_p_value |
MLOG10P |
non_effect_allele |
NEA |
NON_EFFECT_ALLELE |
NEA |
Nsample |
N |
num_samples |
N |
OBS_CT |
N |
odds_ratio |
OR |
OR |
OR |
OR_95L |
OR_95L |
OR_95U |
OR_95U |
other_allele |
NEA |
p |
P |
P |
P |
P.value |
P |
p.value |
P |
P_BOLT_LMM |
P |
p_value |
P |
P_VALUE |
P |
POS |
POS |
Pos |
POS |
pos |
POS |
PVAL |
P |
Pval |
P |
Pval_Estimate |
P |
Pvalue |
P |
Q |
Q |
Q.pval |
P_HET |
Q_df |
DOF |
Q_pval |
P_HET |
R2 |
INFO |
r2 |
INFO |
ref_allele |
REF |
RSID |
rsID |
rsid |
rsID |
rsID |
SNPID |
Rsq |
INFO |
sample_size |
N |
se |
SE |
SE |
SE |
se_c |
SE |
sebeta |
SE |
SNP |
SNPID |
snp |
SNPID |
SNPID |
SNPID |
snpid |
SNPID |
standard_error |
SE |
STATUS |
STATUS |
StdErr |
SE |
T |
T |
T_STAT |
T |
TEST |
TEST |
TotalSampleSize |
N |
TRAIT |
TRAIT |
U95 |
BETA_95U |
variant_id |
SNPID |
Z |
Z |
z |
Z |
Z_Estimate |
Z |
| ## 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 |
|
|
|