I am using gatk-126.96.36.199 version with following command, however I am getting error. please advice....
gatk-188.8.131.52$./gatk HaplotypeCaller -R /home/kumarm/allan-work/RNASEq-alignment/ref_sequence.fasta -I /home/kumarm/allan-work/RNASEq-alignment/sorted-out-align.bam.bai -O /home/kumarm/allan-work/RNASEq-alignment/raw_variants.vcf
A USER ERROR has occurred: Input files reference and reads have incompatible contigs: No overlapping contigs found.
reference contigs = [KF267450.1]
reads contigs = 
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