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Reserved headers

Here is a list of all headers (gl.Sumstats.data) used in GWASLab functions. These headers are fixed to avoid ambiguity within GWASLab framework.

Header Keyword of args in preformat Datatype Description Note
SNPID snpid string variant ID (CHR:POS:NEA:EA) GWASLab assumes EA=ALT and NEA=REF
rsID rsid string dbSNP rsID -
CHR chrom Int64 chromosome number (X 23, Y 24, MT 25) -
POS pos Int64 base pair position -
EA ea category effect allele -
NEA nea category non-effect allele -
STATUS status category 7-digit variant status lookup_status() to check
REF ref category reference allele in reference genome -
ALT alt category alternative allele -
EAF eaf float64 effect allele frequency -
RAF raf float64 reference allele frequency (from reference VCF/BCF file) typically annotated by infer_strand2() or annotate_sumstats()
NEAF neaf float64 non-effect allele frequency -
MAF maf float64 minor allele frequency if EAF, use fill_data to get MAF
DAF daf float64 difference in allele frequency (EAF - ALT_AF from reference VCF) this DAF is not the derived allele frequency
INFO info float32 imputation INFO/RSQ -
BETA beta float64 effect size beta -
SE se float64 standard error of beta -
BETA_95U beta_95U float64 upper bound of beta 95% condidence interval -
BETA_95L beta_95L float64 lower bound of beta 95% condidence interval -
OR OR float64 odds ratio -
OR_95U OR_95U float64 upper bound of OR 95% condidence interval -
OR_95L OR_95L float64 lower bound of OR 95% condidence interval -
HR HR float64 hazard ratio -
HR_95U HR_95U float64 upper bound of HR 95% condidence interval -
HR_95L HR_95L float64 lower bound of HR 95% condidence interval -
CHISQ chisq float64 chi square -
Z z float64 z score -
T t float64 t statistics -
F f float64 F statistics -
P p float64 P value -
P_MANTISSA p_mantissa float64 P mantissa -
P_EXPONENT p_exponent float64 P exponent -
MLOG10P mlog10p float64 -log10(P) -
SNPR2 snpr2 float64 per variant R2 -
DOF dof Int64 degree of freedom -
P_HET phet float64 heterogeneity test P value -
I2_HET i2 float64 heterogeneity I2 -
I2 i2 float64 heterogeneity I2 (alias for I2_HET) -
DIRECTION direction string direction of effect (+, -, ?) -
DENSITY density Int64 signal density -
N n Int64 total sample size -
N_CASE ncase Int64 number of cases -
N_CONTROL ncontrol Int64 number of controls -
N_EFF neff float64 Effective sample size -
GENENAME string nearest gene symbol -
CIS/TRANS string whether the variant is in cis or trans region Cis,Trans,NoReference
DISTANCE_TO_KNOWN Int64 distance to nearest known variants -
LOCATION_OF_KNOWN string relative location to nearest known variants Same,Upstream,Downstream,NoReference
KNOWN_ID string nearest known variant ID -
KNOWN_PUBMED_ID string pubmed ID of the known variant -
KNOWN_AUTHOR string author of the study -
KNOWN_SET_VARIANT string known set and overlapping variant -
KNOWN_VARIANT string known variant overlapping with the variant -
KNOWN_SET string variant set of the known variant -
NOVEL string if the identified variants are novel -
PIP pip float64 Posterior Inclusion Probability -
CREDIBLE_SET_INDEX credible_set_index Int64 credible sets index -
N_SNP n_snp Int64 number of variants included in this locus for finemapping -
LOCUS locus string locus name, usually the lead variant of the locus -
STUDY study string study name -
TEST test string test type -
BETA_RANDOM beta_random float64 random effects beta -
SE_RANDOM se_random float64 random effects standard error -
Z_RANDOM z_random float64 random effects z score -
P_RANDOM p_random float64 random effects P value -