Hey, I have a question here and want suggestions from anyone who did this before I go further.
I have produced a variant VCF with many samples using GATK pipeline. Following steps will include like 1) Select two samples out of a VCF with many samplesSelect a sample 2) exclude non-variant loci 3) filtered lociSelecting homozygote calls using SelectVariants. Seems like this is not so hard by reading instructional documents from GATK website. However, I am not sure should I have annotation on this VCF file before I go ahead to use SelectVariants or it does not matter which one goes first? I do have expression that there is no Rush to do annotation until i get final variant VCF file, am I right?