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An error in the GATK4 GetPileupSummaries
I have been trying to follow the steps outlines by this tutorial https://drive.google.com/drive/folders/0BzI1CyccGsZicXl0anMwQnFYVEU. Everything worked fine but then I got stuck at the GetPileupSummaries step. I keep getting a java error after running the following command.
./gatk-launch GetPileupSummaries -I myBamFile.bam -V gnomad.exomes.r2.0.1.sites.vcf.gz -O output/out.tbl
Here is part of the error message that I keep getting:
13:02:47.898 INFO GetPileupSummaries - Shutting down engine
[October 8, 2017 1:02:47 PM AST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.01 minutes.
java.lang.NumberFormatException: For input string: "."
I am not sure if this is a GATK bug. It looks like is something to do with the vcf file I downloaded from GNomad site.
I appreciate if someone can recommend a solution around this issue.