credtools munge

Clean and standardize GWAS summary statistics.

credtools munge INPUT_CONFIG OUTPUT_DIR [OPTIONS]

Common Use

credtools munge population_config.tsv work/munged --force

Inputs

INPUT_CONFIG can be:

• a population config TSV with popu, cohort, sample_size, and path,
• one summary statistics file path,
• comma-separated summary statistics file paths.

Options

Option	Meaning	Default
--config	JSON column mapping file	none
--force	overwrite existing output files	off
--interactive	create a mapping interactively	off
--log-file	write logs to a file	none

Outputs

OUTPUT_DIR/
- {popu}_{cohort}.munged.txt.gz
- sumstat_info_updated.txt

sumstat_info_updated.txt is the usual input to credtools chunk.

Notes

Munging creates the SNPID column and normalizes common columns such as chromosome, position, alleles, beta, standard error, p-value, and sample size.