I have a multisample vcf file from a study species with a pretty fragmented reference genome. I already applied the basic filtering steps to my vcf using vcftools. 1- Sample filtering: filter out low coverage samples 2- Site and genotype filtering with the following vcftools parameters: --minDP 3 --max-missing 0.8 --maf 0.05 I am now trying to run imputation of missing genotypes using BEAGLE 5.1 and it is running smoothly until it reaches a small scaffold that only has 1 position in the vcf. So clearly I need to erase scaffolds with too few positions from my vcf file, but here is my question: how many positions per scaffold is too few? I tried to look into the BEAGLE documentation but I couldn't find an answer, hopefully someone here can help?!
