A lot of sequencing programs and analyses require a reference genome FASTA file to run. Since I didn't have a reference genome in my possession, I looked into making one of my own. Here is the code I used to create an indexed reference sequence file from the UCSC ftp site that would be compatible with GATK. When concatenating the chromosomes together, make sure they are in the same order and the same length as the .bam file you want to use it with.
After running GATK for the first time, a hg.19.dict file is also created.
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