I have numerous samples which were sequenced, and then genotyped, resulting in two VCF with the same samples in each. I am hoping to calculate the percentage concordance between the files on a sample by sample basis. I have used the snpEff/snpsift concordance command, but I do not understand the column headings of the output file. Any help in understanding the meaning of these headings and/or advice on which columns to use when calculating concordance would be greatly appreciated.
The output column headings are as follows;
output column headings;
can you please tell me if you figured out what those represent and how to interpret the result?