All other parameters were set to default values. We set the khap parameter of IMPUTE2 to 1,000. 7), which chooses a custom reference panel for each study individual for each 2-Mb segment of the genome. Imputation was carried out using IMPUTE2 (ref. This is what my co-authors and I describe as "aggregate R2" in the methods section of, reproduced below: In the column dosage r-squared, the values are probably calculated by creating a vector of all dosages for the SNPs in the bin across all samples in the first VCF, and the same vector in the second VCF, and calculating the Pearson correlation coefficient between those two vectors.Dosage for a genotype is calculated by the formula: GP + 2*GPĮxample 1: a genotype with RR,RA,AA genotype probabilities 0.2,0.3,0.5 has dose 0.3 + 2*0.5 = 1.3Įxample 2: a genotype with only GT field of 0/1 has dose 1Įxample 3: a genotype with only GT field of 1/1 has dose 2.Each line starting with GCsAF is the result of binning SNPs by non-reference allele frequency.I came across this issue while trying to see if a bug had already been reported, but I think I can help out a little.Ĭan you please tell me how to assess the output ofīcftools stats -s samples > cmp.statsįrom GCsS, Genotype concordance by sample (SNPs)' section ?
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