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GATK error message: Badly formed genome location

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!

gatk genotype calling
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written by jtwalker • jtwalker

In the forum post, the problem is that the command he used stated that the chromosome names are indicated only by numbers, so 1,2,3... instead of chr1, chr2, chr3. Instead of -L 20 he should've used -L chr20. You should check if the contig names in your fasta and VCF do match. If not, there is your problem.

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written by ATpoint ATpoint

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