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.
I was running SnpSift for concordance and I got this for example for one subject, can you please help me understand how and which variables here are the most important to determine subject genotype concordance between two vcf files