hi I want to find depth of coverage in one position, for that I used GATK tools, but I give one error like this: Using reference file.... i saw this error again when i wanted to perform variant calling. how i can remove this error? i mean how i can use refrence file in these tools?
GATK is very specific about the types of accepted inputs. I suspect the core problem has to do with the input formatting, a genome mismatch, or content of the reference data. This could be an issue between inputs or with at least one of the inputs. How to format inputs and other expected contents are described at the GATK website/manual help.
That said, even if corrected, the tools may still fail (but for a different reason). All Galaxy-wrapped GATK tools have been deprecated and should be avoided. Any help from the GATK support areas will be focused on the latest GATK build (which is not wrapped).
Instead, please try the alternative methods described in the Variant analysis tutorials here: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team