I was hoping that someone might be able to help me resolve this error I have been encountering while trying to use DOC. It says that "chr1_KI270762v1_alt" is not found in the sequence dictionary.
I run the command as follows:
gatk DepthOfCoverage -R hg38.fasta -I sample.final.bam -O DepthOfCoverage -L hg38.interval_list
The chromosomes are named the same way in all my files (i.e. chr1 chr2...) and 'chr1_KI270762v1_alt' is found in both my .fasta and .dict files. It is also in the .bam file and I guess this is the source of the error. The command I used to create the interval list was:
gatk BedToIntervalList -I hg38.interval.bed -O hg38.interval_list -SD hg38.dict
I reviewed similar posts and have not been able to find a solution that works for me.
Version I am using:
The Genome Analysis Toolkit (GATK) v220.127.116.11
HTSJDK Version: 2.24.1
Picard Version: 2.27.1
Entire program log:
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