Merge branch 'master' of https://github.com/kkmann/impute-gene-expression

README.md

+# Impute gene expression data for CENTER-TBI using PrediXcan
+
+The singularity container is available for download under https://doi.org/10.5281/zenodo.3376504. 
+Data currently needs to be accessed manually due to access restrictions, this workflow should work for enssentially any
+vcf.gz file with dosage (DS) information.
+
+More information on PrediXcan can be found here https://github.com/hakyimlab/PrediXcan and here in the publication:
+
+> Gamazon ER†, Wheeler HE†, Shah KP†, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC, 
+Nicolae DL, Cox NJ, Im HK. (2015) A gene-based association method for mapping traits using reference transcriptome data.
+Nat Genet. doi:10.1038/ng.3367.
+
+We use snakemake to organize the workflow (also pre-installed in the container) and support cluster execution.
+> Johannes Köster, Sven Rahmann, Snakemake—a scalable bioinformatics workflow engine, Bioinformatics, 
+Volume 28, Issue 19, 1 October 2012, Pages 2520–2522, https://doi.org/10.1093/bioinformatics/bts480
+
+## Dependencies
+
+1. linux shell (`bash`), possibly via virtual machine on Windows/Mac 
+2. `wget` (pre-installed or via distribution package manager)
+3. `singularity` container software (tested on 3.3.0) https://sylabs.io/guides/3.3/user-guide
+4. `git`
+
+### Optional
+
+5. python 3.7+ and snakemake 
+6. slurm cluster
+
+## Execution
+ 
+Download and extract the contents of this repository (might be access restricted)
+
+    git clone https://github.com/kkmann/impute-gene-expression
+    cd impute-gene-expression
+
+Download the container image
+
+    bash scripts/download_container.sh
+    
+Execute the workflow inside the container on a single core (takes a while!)
+  
+    singularity exec container.sif snakemake impute 
+    
+Optionally, if snakemake is installed, the workflow can be run in parallel via
+  
+    snakemake --use-singularity -j 8 impute
+    
+where '8' can be replaced by the number of available cores.
+