Germline
Forum thread to discuss GATK Germline tools
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erro in VQSR (WGS)0 votes 1 comment
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Has too many alleles in the combined VCF record0 votes 1 comment
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FastaAlternateReferenceMaker creating chimera0 votes 1 comment
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variant calling: dict and indexing0 votes 1 comment
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Missing RawGtCount annoation from GenotypeGVCF output0 votes 5 comments
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GATK gCNV Calling pipeline error0 votes 0 comments
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genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file Answered0 votes 9 comments
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DetermineGermlineContigPloidy with exome germline data Answered0 votes 24 comments
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Unable to trim uncertain bases without flow order information0 votes 0 comments
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GenotypeGVCFs : VariantQueryProcessorException0 votes 5 comments
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HaplotypeCaller interval list0 votes 1 comment
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Howto call germline SNPs from reads with MAPQ=00 votes 0 comments
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Varinat PASS given Genotype quality = 00 votes 2 comments
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Input configuration for GATK4-gCNV workflow on Terra Answered0 votes 5 comments
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humanG1Kv37 (b37) to hg38 liftover issues0 votes 6 comments
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JointGenotyping.ImportGvcfs terminates without an active exception0 votes 4 comments
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gCNV SVLEN question0 votes 4 comments
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Cohort_denoising.py parameter issue in GermlineCNVCaller Answered0 votes 15 comments
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Jointgenotyping Genomicsdbimport failed for no obvious reasons1 vote 1 comment
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CombineGVCFs 4.1.2.0 throws "java.lang.IllegalArgumentException: Features added out of order:" Answered0 votes 9 comments
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CNNScoreVariants ImportError: cannot import name 'Adam' Answered1 vote 1 comment
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should I worry if the tmp folder not empty after completing GenotypeGVCFs Answered0 votes 1 comment
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Inconsistency between intervals.vcf and Normalized Copy ratios txt file in GCNV workflow 4.2.6.1 Answered0 votes 12 comments
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BaseRecalibrator tool recalibration table Answered0 votes 1 comment
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GATK concordance Answered0 votes 13 comments
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CombineVariants Doesnt produce output0 votes 1 comment
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Funcotator - all IGR classification Answered0 votes 10 comments