Snakemake workflow to reproduce the GWAS analysis on genetic determinants of
E. coli bloodstream infections. Given the sensitive information used as
covariates in this analysis, users wishing to replicate this study should
generate the data contained in the missing data/GWAS_20201217_MEO.csv
file. Summary statistics about each variable can be found as supplementary
material in the preprint.
The input assemblies can be found under the following bioproject accessions:
PRJEB39260 and
PRJEB35745. The fasta
files should be placed inside the data/fastas directory, and annotated GFFs
should be placed inside the data/gffs directory.
To run the three main GWAS analysis (naive, using covariates and burden test) and the power analysis:
snakemake -p annotate_summary map_summary_nc pyseer_rare pyseer_simulation --cores 36 --use-conda
Snakemake will install the appropriate packages for each step as conda environments.
symbolic link to a directory containing the eggnog-mapper database should be
placed in data/eggnog-mapper, as well as a symbolic link to the unzipped fasta
file from uniref50 (data/uniref50.fasta).
Marco Galardini ([email protected])