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sumstats_specification.md

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Summary statistics spec

The results of GWAS are represented as summary statistics, with the following columns:

  • SNP - marker name, for example rs#.
  • CHR - chromosome label
  • BP - base-pair position
  • A1 - effect allele for Z and BETA columns
  • A2 - other allele
  • N - sample size
  • CaseN, ControlN - sample size for cases and controls (logistic regression only)
  • FRQ - frequency of A1 allele
  • Z - z-score (or t-score) of association
  • BETA - effect size; for logistic regression, this contains log(OR)
  • SE - standard error of the BETA column
  • L95, U95 - lower and upper 95% confidence interval of the BETA.
  • P - p-value

For SNP, CHR, BP, A1 and A2 columns the scripts/gwas/gwas.py script will simply copy over the information from the genetic file, i.e. from .bgen or .bim files. This means that SNP is likely to be dbSNP rs#, or some other form of identifyied such as CHR:BP:A1:A2. For CHR and BP, there we don't enforce a specific genomic build - it all depends on what build was used by the genotype data. Finally, A1 and A2 are not guarantied to be minor or major alleles, but A1 will be used as an effect allele for signed summary statistics (i.e. Z and BETA columns).

The sample size N is as reported by the software (plink2 or regenie). For case-control traits, this appears to be a sum of cases and controls (not the effective sample size which would take into account imbalance between cases and controls).

L95 and U95 columns are only provided for plink2 results. CaseN and ControlN columns are only provided for plink2 results for logistic regression. If you need these columns for regenie analysis consider also running plink2 analysis, and copy over the columns into your regenie output.

Comparison of columns names

CoMorMent daner LDSC BioPsyk NORMENT Description
missing ? missing 0 missing good idea to provide this column and referencing a line in .bim file
CHR CHR CHR CHR CHR OK
BP BP BP POS BP keep BP which is more informative ( "POS" could also stand for genomic position )
SNP SNP SNP RSID SNP keep SNP which makes more sense as we copy over marker name from genetic file
A1 A1 A2 EffectAllele A1 keep A1 for consistency with LDSC even thought EffectAllele is more informative
A2 A2 A2 OtherAllele A2 keep A2 for consistency with LDSC even though OtherAllele is more informative
P P P P PVAL OK
SE SE SE SE SE OK
L95 ? missing ORL95 missing keep "L95" as confidence interval may also be for the BETA or LOG(OR)
U95 ? missing ORU95 missing keep "U95"
N ? N N N OK
CaseN Nca N_CAS CaseN NCASE OK
ControlN Nco N_CON ControlN NCONTROL OK
INFO INFO INFO INFO INFO OK
Direction Direction missing Direction DIRECTION OK
BETA BETA or OR BETA B BETA or OR keep "BETA" for consistency with LDSC (and also BETA is more informative)
Z ? Z Z Z OK
FRQ FRQ_A_NNN FRQ EAF FRQ keep "FRQ" which makes more sense for non-EUR populations
missing ? missing EAF_1KG missing not needed

Change log

  • v0.9 - first version of this document