Entering edit mode
6.7 years ago
jtwalker
▴
20
I'm trying to run several hundred samples through GATK's GenotypeGVCFs tool. When doing so I recieved this error message:
<h5>ERROR MESSAGE: Badly formed genome location: Contig 024218.1 given as location, but this contig isn't present in the Fasta sequence dictionary</h5>
I found a post on the GATK forums (https://gatkforums.broadinstitute.org/gatk/discussion/2987/problem-with-reference-genome-in-variant-calling) that seems relevant to my problem, but I still don't really understand what the problem is based on the way that the forum describes it.
Can anyone tell me what I'm doing wrong?
Thanks!
