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4. Cleaning
After parsing and harmonization the reformatted data will be cleaned based on the settings provided in metagwastoolkit.conf. Cleaning settings include:
- MAF, minimum minor allele frequency to keep variants, e.g. default = "0.005"
- MAC, minimum minor allele count to keep variants, e.g. default = "30"
- HWE, Hardy-Weinberg equilibrium p-value at which to drop variants, e.g. default = "1E-6"
- INFO, minimum imputation quality score to keep variants, e.g. default = "0.3"
- BETA, maximum effect size to allow for any variant, e.g. default = "10"
- SE, maximum standard error to allow for any variant, e.g. default = "10"
The resulting file, dataset.cdat, will be used for downstream plotting and analysis.
Copyright (c) 2015-2022 Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com | swvanderlaan.github.io.
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