it's a common error (e.g: GATK: Input files reads and reference have incompatible contigs: No overlapping contigs found ) , as the message said:

Input files reads and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information.

I'm closing this one.

Hello pinnintilikithreddy!

We believe that this post does not fit the main topic of this site.

duplicate

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Hello pinnintilikithreddy!

Questions similar to yours can already be found at:

• Gatk Alignertargetcreator Error
• GATK: Input files reads and reference have incompatible contigs: No overlapping contigs found
• Error when trying to fix the contigs order in the reference and vcf for FastaAlternateReferenceMaker

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: duplicate