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Questions about --sample_ploidy, --indel_heterozygosity, and --heterozygosity
I worked on a uncommon species, of which reference is organized within scaffolds but chromosomes?
Do I still need to set --sample_ploidy?
For --sample_ploidy and --indel_heterozygosity,
If I can use the default settings in case of unknown heterozygosity for the population I'm interested with. If I found there are significantly higher heterozygosity in the result, do I need to re-call the variants by setting the new heterozygosity?