With the failing chromosomes I am able, per previous attempts, to import each of the VCFs individually (i.e., a list of one element). Potentially we can therefore get around this problem by unioning, but we’ve seen that scales quadratically, so it probably won’t be tractable.
I then tried increasing the number of VCFs per chromosome import to 2, taking a random sample from the VCFs available for said chromosome. This failed for Chr1, 15, 22, X and Y in the first run; when I tried again – because the subset is random – Chr1 and 15 went through OK, while the other three still failed… After multiple trials, all chromosomes succeed for some random subset of size 2.
This suggests to me that there is something wrong with particular VCF files, regardless of the chromosome. However, the fact that they import individually just fine is super-weird.