A Python tool, based on GWASLab, for assembling a computational pipeline to standardize, QC, harmonize, convert, and plot your summary statistics.
see environment.yml and Makefile
The script needs a configuration file, a summary statistics file and its format as input.
e.g.: python src/gwaspipe.py -c examples/config_ldscore_pipe.yml -i ./data/seq.13392.13_res.gwas.regenie.gz -f regenie
Input format can be: regenie, fastgwa, ldsc, fuma
There are some example configuration files in the examples directory.
Genome: Genome assembly GRCh37.p13
VCF file with allele frequency information for inferring strand and comparing allele frequency: 1kg_eur_hg19