Impute GWAS summary statistics using reference genotype data
Project description
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.
Installation
-
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
cd fizi
thenpython setup.py install --user
or optionally assudo python setup.py install
if you have root access and wish to install for all users -
Check that FIZI was installed by typing
fizi --help
-
If that did not work, and
--user
was specified, please check that your local user path is included in$PATH
environment variable.--user
location and can be appended to$PATH
by executingexport PATH=`python -m site --user-base`/bin/:$PATH
which can be saved in
.bashrc
or.bash_profile
. To reload the environment typesource ~/.bashrc
orsource .bash_profile
depending 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[1]. 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
If you have any questions or comments please contact nmancuso@mednet.ucla.edu and/or meganroytman@gmail.com
For performing various inferences using summary data from large-scale GWASs please find the following useful software:
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