non-human aneuploid VQSR
I am doing variant calling on each chromosome of each of my samples individually, because each sample can have a different ploidy, which also varies between chromosomes.
I am now looking at the VQSR documentation, and I have discovered that I am on my own! One question people might be able to answer though - if I do the variant calling separately, should I do the VQSR separately as well, or can I combine my variants? I am working on a very short genome and I am not expecting a high density of variants...