Hi, I am interested in doing demographic inference $ quantifying+id deleterious variants. I have assembled a genome for this. Because demographic inference is my most important topic, I focus on having a reference for that - which is having only autosomes- hence, I eliminated the potential/likely X $ Y related scaffolds.
So now I am questioning the impact of this on the functional annotation $ effect predictor.
Can I annotate the full genome and can I later use the vcf made with the autosome-only reference to find the deleterious variants? oR should I annotate the full genome $ use it for variant calling, and later somehow excluding the non-autosome snps for demographic inference?
I am new in genomic manipulating so I am unsure how to achieve this!
Thanks!
