Selectvariants And Annotation Of Variants With Vcf Format

Question

[Tonyzeng]

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?

Thank you

Answer 1

[Sean Davis]

I tend to do annotation before doing any filtering so that I have the annotation available at all stages of analysis, but for your case as described, it seems the annotation can go in whenever you need it and that could be after your three steps.

[Tonyzeng]

Thank you , Sean