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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An issue with detecting a big deletion with copy number calling pipeline0 votes 2 comments
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java.lang.ArrayIndexOutOfBoundsException error while using HaplotypeCaller0 votes 12 comments
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Multisample Tumor Only Copy Number Analysis0 votes 1 comment
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Using HaplotypeCaller for metagenomic viral assembly0 votes 1 comment
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No output file was generated with MarkduplicatesSpark command0 votes 1 comment
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Using GATK4 to make phased VCF files0 votes 1 comment
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GenotypeGVCFs no output0 votes 2 comments
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how to remove FFPE artifacts from Single cell FFPE cell cancer samples0 votes 2 comments
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Haplotypecaller terminate with ExitCode 245, but without error0 votes 3 comments
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Issue with GenomicsDBImport on very large chromosomes0 votes 3 comments
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GATK VariantFiltration NumberFormatException when reading decimal values0 votes 1 comment
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CollectSVEvidence failing for some bam files0 votes 1 comment
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How to make filename.gtf.idx?0 votes 1 comment
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why get a HTTP error0 votes 1 comment
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TagGermlineEvents hg38, GATK version0 votes 2 comments
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Consolidating tetraploid GVCFs for joint calling Answered0 votes 3 comments
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gatk pileup result lost some reads cover?1 vote 2 comments
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splice variants are missing from the Mutect2 output0 votes 3 comments
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Interrupted using gatk call HIFI SNP, and Confusing gvcf merge results.0 votes 5 comments
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Picard MarkDuplicates on paired-end sequencing data from a TIPseq experiment0 votes 2 comments