modules/glimpse2_concordance
Program to compute the genotyping error rate at the sample or marker level.
Input
Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions.
chrXX:leftBufferPosition-rightBufferPosition Validation dataset called at the same positions as the imputed file.
*.{vcf,bcf,vcf.gz,bcf.gz} Alternative to frequency bins, group bins are user defined, provided in a file.
*.{txt,tsv} Allele frequency bins used for rsquared computations.
By default they should as MAF bins [0-0.5], while
they should take the full range [0-1] if —use-ref-alt is used.
0 0.01 0.05 ... 0.5 User-defined allele count bins used for rsquared computations.
1 2 5 10 20 ... 100000 Default allele count bins used for rsquared computations.
AN field must be defined in the frequency file.
Minimum genotype likelihood probability P(G|R) in validation data.
Set to zero to have no filter of if using –gt-validation
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 Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype.
*.rsquare.spl.txt.gz 