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GetPileupSummaries - ERROR Badly formed genome unclippedLoc
I am getting the following error (pasted below) running GetPileupSummaries.
I used hg38 without alternative contigs !
I am running GATK 188.8.131.52 and I strictly followed GATK best practice for Mutect2 (but I don't use alternative contigs).
Thx a lot
GetPileupSummaries - Initializing engine
14:19:52.446 INFO FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/CRU/afranceschini/htsflow/data/input/genomes/hg38/dbsnp/biallelic_hg38_af-only-gnomad.vcf.gz
14:19:52.681 INFO FeatureManager - Using codec VCFCodec to read file file:///hpcnfs/scratch/CRU/afranceschini/htsflow/data/input/genomes/hg38/dbsnp/biallelic_hg38_af-only-gnomad.vcf.gz
14:33:32.019 INFO GetPileupSummaries - Shutting down engine
[May 16, 2019 2:33:32 PM CEST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 13.70 minutes.
A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr1_KI270766v1_alt given as location, but this contig isn't present in the Fasta sequence dictionary
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.