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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Exec format error in unmapped bam file0 votes 1 comment
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Where do I find GATK v2.8-1?0 votes 6 comments
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Mutect2 freezes at FeatureManager - Using codec VCFCodec to read file0 votes 1 comment
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HaplotypeCaller and Mutect2 used for SARS-Cov-20 votes 2 comments
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calling large scale structural variants Answered0 votes 1 comment
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GATK4.0.3.0 GenotypeGVCFs - Could not open array genomicsdbarray0 votes 8 comments
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How do I tell FastaAlternateReferenceMaker to only replace properly called sites? Answered0 votes 5 comments
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GetPileupSummaries raised an error: htsjdk.tribble.TribbleException Answered0 votes 1 comment
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Support hg38 on Mutect (not Mutect2) Answered0 votes 3 comments
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PoN deidentification Answered0 votes 4 comments
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Best practice for using Mutect2 in serial tumor samples from same patient0 votes 10 comments
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PhaseByTransmission is not running through all the chromosomes0 votes 3 comments
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Consolidate structural variants from multiple samples in one VCF Answered0 votes 1 comment
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Mutect for Somatic SNVs in Highly Polymorphic Genome Regions1 vote 2 comments
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How do I run CreateExtendedIlluminaManifest myself (for GtcToVcf) for a customized Illumina chip? Answered0 votes 2 comments
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ASEReadCounter error: missing the read group (RG) tag Answered0 votes 2 comments
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How to run BwaMemIndexImageCreator on large input? Answered0 votes 9 comments
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CombineGVCFs, java heap space, and ploidy Answered0 votes 2 comments
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java.lang.ArrayIndexOutOfBoundsException: 32772 while running GenotypeGVCFs Answered0 votes 17 comments
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Argument variant missing from FastaAlternateReferenceMaker0 votes 0 comments
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Argument variant missing from FastaAlternateReferenceMaker Answered0 votes 5 comments
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GATK Variant Calling in RNA-seq Answered0 votes 2 comments
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Gatk Variant filtration for strand-specific RNA-seq library Answered0 votes 1 comment
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SNP VCF file and bamout not the same Answered0 votes 11 comments
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Picard MarkDuplicates get killed0 votes 3 comments
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ASEReadCounter ouputs only header0 votes 10 comments
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How to do PSMC with GATK4.0 Answered0 votes 1 comment
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Mutect2 for Pool-seq ? Answered0 votes 3 comments
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"Could not determine local host name"0 votes 1 comment