Hi everyone, 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: ''hg38_v0_HybSelOligos_whole_exome_illumina_coding_v1_whole_exome_illumina_coding_v1.Homo_sapiens_assembly38.targets.interval_list''
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?
I strongly recommend you download the FAI and DICT files from the GATK Resource bundle as well. I had the same errors with the dictionary that I made by myself.