Impute GWAS summary statistics using reference genotype data
Functionally-informed Z-score Imputation (FIZI)
FIZI leverages functional information together with reference linkage-disequilibrium (LD) to impute GWAS summary statistics (Z-score).
This README is a working draft and will be expanded soon.
Make sure that setuptools is up-to-date by typing the following command
pip install setuptools --upgrade --user
First grab the latest version of FIZI using git as
git clone https://github.com/bogdanlab/fizi
FIZI can be installed using setuptools as
python setup.py install --useror optionally as
sudo python setup.py installif you have root access and wish to install for all users
Check that FIZI was installed by typing
If that did not work, and
--userwas specified, please check that your local user path is included in
--userlocation and can be appended to
export PATH=`python -m site --user-base`/bin/:$PATH
which can be saved in
.bash_profile. To reload the environment type
source .bash_profiledepending where you entered it.
Incorporating functional data to improve summary statistics imputation
Usage consists of several steps. We outline the general workflow here when the intention to perform imputation on chromosome 1 of our data:
Munge/clean all GWAS summary data before imputation
fizi munge gwas.sumstat.gz --out cleaned.gwas
Partitioning cleaned GWAS summary data into chr1 and everything else (loco-chr1).
Run LDSC on locoChr to obtain tau estimates
Perform functionally-informed imputation on chr1 data using tau estimates from loco-chr
Imputing summary statistics using only reference LD
When functional annotations and LDSC estimates are not provided to FIZI, it will fallback to the classic ImpG algorithm described in ref. To impute missing summary statistics using the ImpG algorithm simply enter the command
fizi impute cleaned.gwas.sumstat.gz plink_data_path --chr 1 --out imputed.cleaned.gwas.sumstat
Software and support
For performing various inferences using summary data from large-scale GWASs please find the following useful software:
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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