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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How do I use BQSR if I do not have a list of known sites?0 votes 3 comments
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GetPileupSummaries Error: java.lang.OutOfMemoryError: Java heap space0 votes 4 comments
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disable_read_filter function cannot be disabled0 votes 8 comments
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Error when attempting to filter by 'DP'0 votes 2 comments
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CombineGVCFs, Java heap space Error0 votes 1 comment
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Gencode annotation "errors" Answered-1 votes 1 comment
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Variant level quality metrics0 votes 6 comments
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how to combine mutect2 and haplotypecaller vcfs from the same sample Answered0 votes 7 comments
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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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Trio Denovo annotation using VariantAnnotator PossibleDenovo not working? Answered0 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 patient Answered0 votes 11 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 Regions Answered1 vote 3 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