Badly formed genome unclippedLoc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary

1

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:

  1. Does anyone know if there is any release date for this hg38 based exome interval file?
  2. Or the file I put is ok and the error is coming from somewhere else?


Mutect2


GATK


Variant


WES


GenomicsDB


calling

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