What are SNPEFF and GT in vcf files? Im sorry to ask this but I have little experience in Bioinformatics and Genomics, I'm in the process of learning but I'm not there yet. Im trying to work with a couple of vcf files containing the original exome data and two imputations for chromosome 5, Im trying to find a way to graph the associations between the accuracy of the imputation (in the form of comparing occurrences of 0/1, 1/1, 1,0 and NA) and the SNPEFF Functional Class in the form of either None, Silent, Nonsense, and Missense. I also want to try and do something with the allele frequency of the same file but Im not sure where to start as Im not familiar with SNPEFF and the terminology of vcf files.
Any help would be a life saver thankyou.
Could you please add more information? I'm not sure what you're doing.
Do you mean you're trying to comparing the occurrences of 0/1, 1/1, 1,0 and NA between the imputed and not imputed vcf file?