CLI Reference

This section is for lookup. If you are learning the workflow, use the tutorials first.

Commands

Command	Use it when
credtools munge	raw summary statistics need cleaning and standard column names
credtools chunk	genome-wide files need to be split into loci
credtools prepare	chunked locus files need LD matrices from genotype references
credtools meta	you want to run meta-analysis as a separate step
credtools qc	you want standalone QC tables or cleaned inputs
credtools finemap	you want standalone fine-mapping
credtools pipeline	you want meta-analysis, QC, and fine-mapping in one run
credtools plot	you want quick QC or result plots

General flags:

credtools --help
credtools --version
credtools --log-file credtools.log

Command-specific help:

credtools prepare --help
credtools pipeline --help
credtools finemap --help

Use the long flag in scripts

Short flags are handy at the terminal. Long flags make scripts easier to read six months later.