Germline
Forum thread to discuss GATK Germline tools
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Input configuration for GATK4-gCNV workflow on Terra0 votes 1 comment
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Error in merged bam files0 votes 1 comment
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In CNV Caling, why the intervals in two batches are not consistent?0 votes 1 comment
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Format error in unmapped bam file0 votes 2 comments
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run into PythonScriptExecutorException when executing PostprocessGermlineCNVCalls about positional arguments Answered0 votes 1 comment
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CNNScoreVariants + GPU Answered0 votes 2 comments
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why I have a 1/1 genotype on chromosome X for males Answered0 votes 5 comments
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combineGVCF errors and questions: inconsistent references & combineGVCF twice0 votes 16 comments
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DetermineGermlineContigPloidy with exome germline data Answered0 votes 23 comments
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Sample replicates in gCNV workflow Answered0 votes 4 comments
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gatk DBImport error Answered0 votes 1 comment
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Jointgenotyping on terra Answered0 votes 1 comment
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Het call from HaplotypeCaller in cases of low read support in input bam Answered0 votes 5 comments
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GenotypeGVCFs is too long Answered0 votes 3 comments
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GenomicsDBImport: variants have the same position in Gvcf file Answered0 votes 3 comments
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Error while running GATK4 germline workflow Answered0 votes 1 comment
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GenomeStrip: CNVs in segmentally duplicated regions Answered0 votes 3 comments
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How to speed up GenomicsDBImport when dealing with a huge dataset? Answered0 votes 4 comments
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Caused by: java.util.zip.ZipException: Not in GZIP format0 votes 1 comment
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Error running DenoiseReadCounts on arm64 processor Answered0 votes 5 comments
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Variant not called with HaplotypeCaller Answered0 votes 14 comments
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Haplotypecaller : variant calling not seen in bamout alignments Answered0 votes 14 comments
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Haplotypecaller too long ? Answered0 votes 5 comments
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sample DP(read coverage) is large but the genotype is ./. Answered0 votes 5 comments
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can't generate .segment.vcf.gz when use PostprocessGermlineCNVCalls Answered0 votes 1 comment
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fail to execute GermlineCNVCaller Answered0 votes 1 comment
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ApplyVQSR AS_FilterStatus=VQSRTrancheSNPXXXXtoXXXX but variant still passes FILTER Answered0 votes 3 comments
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fail to execute DetermineGermlineContigPloidy Answered0 votes 1 comment
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BaseRecalibrator java.lang.NullPointerException Answered0 votes 3 comments
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WholeGenomeGermlineSingleSample, hg38 reference, missing contamination resources Answered0 votes 1 comment