Heng Li posted several issues with the human reference genomes given in these resources and suggests the following compressed FASTA file to be used as hg38/GRCh38 human reference genome.
if you map reads to GRCh38 or hg38, use the following:
There are several other versions of GRCh37/GRCh38. What’s wrong with them? Here are a collection of potential issues:
More at http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
