Special GATK Use Cases
Information here covers items that are not in Best Practices but may someday be a part of Best Practices
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use_jdk_deflater not defined?0 votes 0 comments
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Using gatk VariantFiltration to filter ONT wf-artic generated VCF files0 votes 2 comments
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Read Group (UNKNOWN) is not a recognized platform1 vote 1 comment
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CombineGVCFs - elements of input iterator not sorted Answered0 votes 2 comments
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gatk CombineGVCFs Answered0 votes 2 comments
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BaseRecaliberator .fai file error0 votes 1 comment
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RAD-seq Variant calling0 votes 1 comment
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GATK error Answered0 votes 4 comments
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GATK HaplotypeCaller issues with Genotyping (GT)0 votes 1 comment
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HaplotypeCaller output not generated, no error Answered0 votes 1 comment
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DepthOfCoverage Output Files Empty - mtDNA0 votes 1 comment
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incomplete output when running ASEReadCounter Answered0 votes 5 comments
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Monomorphic sites after GenotypeGVCFs --include-non-variant-sites0 votes 2 comments
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HaplotypeCaller not writing output Answered0 votes 1 comment
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--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' Answered0 votes 1 comment
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Standalone HaplotypeCaller Answered0 votes 5 comments
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Genotype concordance - dictionaries are not the same size Answered0 votes 1 comment
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java.lang.ArrayIndexOutOfBoundsException: 32770 while using GenotypeGVCFs Answered0 votes 1 comment
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Find variants with HaplotypeCaller on MAPQ0 regions0 votes 1 comment
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no read counts per allele while using gatk ASEReadCounter Answered0 votes 11 comments
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--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' Answered0 votes 8 comments
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genomicsdbimport add new samples Answered0 votes 2 comments
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PathSeqPipelineSpark: Failed to map segment from shared object ERROR Answered0 votes 2 comments
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GATK concordance Answered0 votes 22 comments
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issue while running mitochondrial analysis Answered0 votes 15 comments
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Aligning very short reads Answered0 votes 2 comments
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depth of coverage total summary should not be 100.0 Answered0 votes 7 comments