modules/glimpse_concordance
Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.
Description
Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset.
Input
Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
chrXX:leftBufferPosition-rightBufferPosition Validation dataset called at the same positions as the imputed file.
*.{vcf,bcf,vcf.gz,bcf.gz} Minimum coverage in validation data.
If FORMAT/DP is missing and —minDP > 0, the program exits with an error.
Output
Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.
*.errors.cal.txt.gz Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.
*.errors.grp.txt.gz Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype.
*.errors.spl.txt.gz Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.
*.rsquare.grp.txt.gz maintainer
