Of course, one should use
hs37d5.fa for read mapping.
However, should I bother to call variants on the decoy contig
hs37d5? GATK Haplotype Caller is spending ages on the contig and I will never use the variant calls.
Would this contig be of any use downstream? Would it make sense to use the GATK variant recalibration on the variant calls of this contig or could they be safely ignored?