The GATK uses two files to access and safety check access to the reference files:
a .dict dictionary of the contig names and sizes and a .fai fasta index file to allow
efficient random access to the reference bases. You have to generate these files in
order to be able to use a Fasta file as reference.
java -jar CreateSequenceDictionary.jar R= Homo_sapiens_assembly18.fasta O= Homo_sapiens_assembly18.dict
samtools faidx Homo_sapiens_assembly18.fasta