Hi, I have a non-technical question: What is the advantage of performing a population-level variant calling (samples for all sub-species concurrently) as opposed to individual level (one sample at a time)? What additional info is provided in the former case? Also, I have to do this for ~3000 samples. Is it feasible to perform population level variant calling for all 3000 concurrently? Will it take 3000-times longer than a single-sample? Thanks in advance,
I am working on population samples from fungi. I am aware that the Haplotype Caller is specific for diploid genomes and the UnifiedGenotyper is preferred for population samples. According to the best practices, I would what like to know what -ploidy should be specified while calling variants of population samples?