Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn’t present in the Fasta sequence dictionary
I’m trying to run Mutect2 for WES cancer data.
However, since their Resource bundle only supports h19 seems I cannot proceed (I want to compare it with Strelka2 results).
I’ve been looking for some hg38 interval_list file and I found:
However, when I run the GenomicsDBImport I get the error (no matter if I use my own hg38 reference and .dict or the ones from GATK Resource Bundle):
”A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn’t present in the Fasta sequence dictionary”
So, my questions are:
- Does anyone know if there is any release date for this hg38 based exome interval file?
- Or the file I put is ok and the error is coming from somewhere else?
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