I'm a bit confused about how to proceed for generating a mask for vcf2smc. I'm working with ddRAD data and I have both a filtered and an unfiltered VCF, as well as a BED file with all known repeats in the reference genome. What should my mask consist of? All sites that are not in the filtered VCF? Only sites that were excluded from the unfiltered VCF? Should I include repeat positions (ignored during calling) in my mask?
I'm a bit confused about how to proceed for generating a mask for vcf2smc. I'm working with ddRAD data and I have both a filtered and an unfiltered VCF, as well as a BED file with all known repeats in the reference genome. What should my mask consist of? All sites that are not in the filtered VCF? Only sites that were excluded from the unfiltered VCF? Should I include repeat positions (ignored during calling) in my mask?