qctool v2
A tool for quality control and analysis of gwas datasets.
Processing intensity data
(under construction)
overview
documentation
Diagram of options
List of options
Change history
examples
Basic usage
Converting file formats
Thresholding genotypes
Sorting and reordering data
Combining datasets
Merging in variants
Altering variant identifying data
Using qctool in a pipeline
Filtering samples
Filtering variants
Computing summary statistics
Computing annotations
Adding data to a sample file
Computing LD
Computing principal components
Working with sex chromosomes
file formats
Genotype file formats
Sample file formats
Summary statistic file formats
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