The VCF file output from VCF Combine only has data up until Chromosome 3. I checked the vcf file output from all the other steps I ran up until VCF Combine and the full data (all the chromosomes) was there, so it seems like this tool in particular is eating my data. I tried to run VCFsort on all my VCF files and then try to combine them again (a tip that was given on this forum around a year and a half ago), but the output is the same. What is going on?!
I also saw it suggested to use the Combine Variants tool instead but I'm not sure if this tool achieves the same result and which reference file I'm supposed to input.