JAVA is returning errors when I run Mutect2 (gatk188.8.131.52) in tumor-only mode and tumors-normals mode. The error seems to be driven by the germline-resource. I used a modified version of gnomadV3 on the gnomAD browser. I modified the gnomAD file to have the identical contigs in my BAM files by using bcftools to remove the "chr" and using Picard's UpdateVCFSequenceDictionary and SortVCF to have identical contig order as BAM files.
Below is the list of errors as a iterated through trouble shooting.
1) tumor-only mode with germline resource: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
2) 1) tumor-only mode with germline resource and --af-of-alleles-not-in-resource=alpha/N: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
3) tumors-normals mode with gremline resource: RuntimeIOException: java.io.IOException: Invalid file pointer: 7527921015141675 for /path/mygnomAD.vcf.bgz
4) tumors-normals mode without germline-resource: NO error
I think I need to modify my gnomAD file but I don't understand how.
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