Input Format

This page describes the format of GWAS summary statistics data (specified by the --gcor flag), reference panel (specified by the --bfile flag), annotation files (specified by the --annot flag), LD score files ( specified by the --ref-ld-chr and --w-ld-chr flag), and minor allele frequency files (specified by the --frqfile flag).

GWAS summary statistics data

GWAS summary statistics data should be in plain text or gzipped text format containing the following columns:

  • SNP rs ID of the SNP (e.g. rs62442).
  • CHR Chromosome number of the SNP. This should be a number between 1 and 22.
  • BP Base pair position of the SNP.
  • A1 Effect allele of the SNP. The sign of the Z-score is with respect to this allele.
  • A2 The other allele of the SNP.
  • Z The Z-score of the SNP.
  • N Sample size of the SNP.
Note: This file format is compatible with LDSC. Other columns (e.g. MAF, INFO, etc.) may be included in the file, but will not be used. It is also recommended [although not required] that the summary data files are sorted by their chromosomes and base pairs. All SNPs with either duplicate ID or position will be removed before any analysis.
( Note: It is important that the alleles of each SNP in the GWAS summary statistics file are consistent across the two populations.)

Reference panel

Reference panels should be in PLINK format (specified using the --bfile flag).

The following is a list of publicly available reference panels.

1000 Genomes Project reference genotype data for East Asian and European populations can be downloaded here.

Note: S-LDXR requires the centimorgan information of each SNP to accurate estimation of LD scores.

Annotation files

Annotation files should be in gzipped text format. The first 4 columns should always be:

  • CHR Chromosome number of the SNP.
  • BP Base pair position of the SNP.
  • SNP rs ID of the SNP (e.g. rs19800731).
  • CM Position of the SNP in centimogan.

The first annotation (usually the base annotation) should start on the 5th column.

baseline-LD-X model annotations can be downloaded here.

LD score files

LD score files should be in gzipped text format. The first 3 columns should always be:

  • CHR Chromosome number of the SNP.
  • SNP rs ID of the SNP (e.g. rs19790919).
  • BP Base pair position of the SNP.

LD scores of the first annotation (usually the base annotation) should start on the 4th column.

Note: The regression weight file (specified by the --w-ld-chr flag) has the same format as LD score files.

LD scores for the baseline-LD-X model annotations can be downloaded here.

Minor allele frequency files

Minor allele frequency files format is the same as that of PLINK. The columns are:

  • CHR Chromosome number of the SNP.
  • SNP rs ID of the SNP (e.g. rs19800301).
  • A1 Non-effect allele.
  • A2 Effect allele (encoded as 1 in PLINK bed file).
  • MAF Minor allele frequency
  • NCHROBS Number of samples times 2.

Minor allele frequency files for the East Asian and European populations can be downloaded here.