Summary Statistic Imputation software

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.


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.