Summary Statistics File Format

Brendan Bulik-Sullivan edited this page Mar 5, 2015 · 3 revisions

This page describes all new file formats introduced for use with the --h2 and --rg flags.

NOTE chromosomes are assumed to be integers. We haven't yet implemented LD Score regression for sex chromosomes


For GWAS data. Whitespace-delimited text, one row per SNP with a header row. Column order does not matter.

We recommend that you convert your summary statistics to the .sumstats format using the program included with ldsc, because checks all the gotchas that we've run into over the course of developing this software and applying it to a lot of data.

Required Columns

  1. SNP -- SNP identifier (e.g., rs number)
  2. N -- sample size (which may vary from SNP to SNP).
  3. Z -- z-score. Sign with respect to A1 (warning, possible gotcha)
  4. A1 -- first allele (effect allele)
  5. A2-- second allele (other allele)

Note that ldsc filters out all variants that are not SNPs and strand-ambiguous SNPs.

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