QCTOOL is a command-line utility program for basic quality control of gwas datasets. It supports the same file formats used by the WTCCC studies, as well as the binary file format described here, and is designed to work seamlessly with SNPTEST and related tools. QCTOOL computes per-sample and per-SNP summary statistics, and uses these to filter out samples and SNPs from the dataset (either by removing them from the files or by writing exclusion lists).
- MacOsX / Linux
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