$GATK HaplotypeCaller -R $ref -L $locations -I Bamfiles.txt -ploidy 1
The user error looks like this:
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found. reference contigs = [All of the correct contigs are listed out] reads contigs = 
Meaning, the reads contigs are being read-in as blank
I thought maybe one of my files was aligned incorrectly. I looked at their headers
for file in $(cat Bamfiles.txt); do samtools view -H $file; done | sort | uniq -c > Out.txt
The counts for each chromosomal header were consistent and the same numbers as I have samples. The only thing that looked different: about 1/4 of my samples (from an earlier study) had VN (sam version): 1.3 while the rest had VN: 1.5. Could this be enough to cause GATK to reject my samples and if so is there an easy way to convert between samfile 1.3 and 1.5 or should I re-align them?