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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Consolidating tetraploid GVCFs for joint calling Answered0 votes 3 comments
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HaplotypeCaller does not work Answered0 votes 2 comments
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CombineGVCFs - elements of input iterator not sorted Answered0 votes 5 comments
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gatk CombineGVCFs Answered0 votes 2 comments
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GATK error Answered0 votes 4 comments
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HaplotypeCaller output not generated, no error Answered0 votes 1 comment
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incomplete output when running ASEReadCounter Answered0 votes 5 comments
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Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites? Answered0 votes 6 comments
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Monomorphic sites after GenotypeGVCFs --include-non-variant-sites Answered0 votes 8 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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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
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picard.PicardException: Start on sequence 'chr1' was past the end: 565891 < 627380 Answered0 votes 1 comment
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Discrepancy between hg38 reference genome version used for sequence alignment vs HaplotypeCaller steps Answered0 votes 2 comments
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HaplotypeCaller does not recognize alternative placement of an indel in a repetitive region Answered0 votes 5 comments
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GVCF vs VCF INFO tags, relevance for filtering RNAseq SNPs Answered0 votes 4 comments
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Genotype several gvcf files at only few thousands positions Answered0 votes 1 comment
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Picard "Too many open files" Answered0 votes 2 comments
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Maximum performance HaplotypeCaller Answered1 vote 10 comments
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Running GATK for detecting translocations in targeted single-cell DNA-seq Answered0 votes 5 comments