Hi! I am facing a problem with the GATK, when I try to use the tools listed before, it always says "No fasta dataset available" but I have imported the .fasta form the GATK bundle and I am unable to run any of the tools of GATK, I review that you say
"Since you are using hg19, the most likely cause for the error is that the reference fasta file you are using is not ordered properly, or that your alignments were made using a different genome (e.g. alignment with bwa using built-in hg19 [not ordered properly] and then GATK using a different hg19 fasta from your history.)"
How do I know if is GATK ordered? Please guide me