I had to compare variant calls from two different arrays. Exome sequence and OMNI chip.
I found genoytpe concordance per sample (sample based Genotype concordance) using "GATK Genotype concordance". The output is shown below which gives overall genotype concordance per sample.
Sample Non-Ref_Sensitivity Non-Ref_Discrepancy Overall_Genotype_Concordance sample1 0.923 0.076 0.997 sample2 0.930 0.082 0.997 sample3 0.914 0.087 0.996
My question is : How to find genotype concordance per SNP/variant?? Where my output would be something like this
SNP Overall_Genotype_Concordance SNP1 0.986 SNP2 0.97 SNP3 0.994
I tried using GATK's -VariantEval tool. This gives only the overall mean concordance rate for all the SNPs, whereas I would like to see concordance rate for every SNP.
Thanks in Advance.