This command-line software enables summary statistics imputation (SSimp) for GWAS summary statistics.

The only input needed from the user are the GWAS summary statistics and optionally a reference panel (if different from the 1000 Genomes) for LD computation.


The compiled binary file for linux and osx can be downloaded from here and the source code from here.


ssimp --gwas gwas/small.random.txt --ref ref/small.vcf.sample.vcf.gz --out output.txt

This will impute the Z-statistics, using a selected reference panel (see section above) and generate a file output.txt, which stores the imputed summary statistics. The txt file assigned to--gwas contains at least the following columns: SNP-id, reference allele, risk allele, Z-statistic, and at least one row.

Note that multiprocessing mode is not yet implemented, hence to speed up computation we recommend splitting up the job to smaller chromosomal chunks using

ssimp --gwas gwas/small.random.txt --ref ref/small.vcf.sample.vcf.gz --out output.txt --impute.range 22:18000000-22:18100075


  1. Run ssimp with no arguments to see the [usage message]
  2. Check out [examples]
  3. Read the [detailed manual] that contains information not present in the usage message.