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pheweb

Overview

Field Value
Format key pheweb
Spec file formats/pheweb.json
Cite name PheWeb
Version 20220928
Last checked 20250106
Source https://github.com/statgen/pheweb
GitHub https://github.com/statgen/pheweb
Citation Gagliano Taliun, S.A., VandeHaar, P. et al. Exploring and visualizing large-scale genetic associations by using PheWeb. Nat Genet 52, 550–552 (2020).
## File layout
Field Value
Separator 'tab, space, or comma'
NA value , ., NA, N/A, n/a, nan, -nan, NaN, -NaN, null, NULL
Header row yes
## Column mapping
Raw header Canonical
#chrom CHR
a1freq EAF
ac N
af EAF
af.cases EAF_CASE
af.controls EAF_CONTROL
alt EA
alternate EA
beg POS
begin POS
beta BETA
bp POS
case_af EAF_CASE
chr CHR
chrom CHR
control_af EAF_CONTROL
frq EAF
maf MAF
marker_id SNPID
n N
n_cases N_CASE
n_controls N_CONTROL
ns N
ns.case N_CASE
ns.ctrl N_CONTROL
num_cases N_CASE
num_controls N_CONTROL
num_samples N
or OR
p P
p.value P
pos POS
pval P
pvalue P
r2 INFO
ref NEA
reference NEA
se SE
sebeta SE
## Notes
  • File can be gzipped
  • Variants must be sorted by chromosome and position, with chromosomes in order [1-22,X,Y,MT]
  • Column names are case-insensitive
  • Reference allele must match the reference genome specified in config.py (hg_build_number 19 or 38)
  • If pval is log10 (e.g., REGENIE output), set pval_is_neglog10 = True in config.py
  • Custom column names can be mapped using field_aliases in config.py

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