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PostsRecent activity by jorgez Sort by recent activity
Hello, b) What does the --max-allowed-low-hets MTLowHeteroplasmyFilterTool parameter mean? the help argument says:Number of low het sites allowed to pass other filters before filtering out all low ...
identify heteroplasmic variants MTLowHeteroplasmyFilterTool
Hello, This is not an error but a How do I... question. How do I separate the variants coming from the major constituent mtDNA from the heteroplasmic variants? I have run the mitochondria-pipeline...
CombineVariants set attribute filters on all callers explicitly (not with filteredInAll)
If you are seeing an error, please provide(REQUIRED) : a) GATK version used: 3.7-0-gcfedb67 b) Exact command used: java -jar $EBROOTGATK/GenomeAnalysisTK.jar -T CombineVariants \-R hg38.fa \--vari...
FixVcfHeader error: A reference dictionary is required for creating Tribble indices on the fly
Hello GATK team, I'm getting an error when using FixVcfHeader. The error complains about a reference dictionary which is required for creating Tribble indices on the fly. Could you please tell me h...
LiftoverVcf fails to lift over a GVCF file. Error java.lang.ArrayIndexOutOfBoundsException: -1
Hello, LiftoverVcf gives me this error java.lang.ArrayIndexOutOfBoundsException: -1 when trying to lift over a gvcf file from hg38 to hg19. I have validated the input vcf file with ValidateVarian...