Germline
Forum thread to discuss GATK Germline tools
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Cohort_denoising.py parameter issue in GermlineCNVCaller Answered0 votes 15 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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Variant filtered from GVCF Answered1 vote 9 comments
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Funcotator - all IGR classification Answered0 votes 10 comments
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Funcotator Misconfigured Error (All IGR Annotations) Answered0 votes 6 comments
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DetermineGermlineContigPloidy error: line 137 Answered0 votes 3 comments
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The same number of SNPS and INDELS identified for all samples after joint genotyping Answered0 votes 12 comments
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SelectVariants error: Multiple Criteria Answered0 votes 3 comments
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B37 joint variant calling workflow says "for hg38 only" Answered0 votes 1 comment
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Program Record ID already in use in unmapped BAM file. Answered0 votes 1 comment
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Haplotypecaller 4.5.2.0 --alleles unexpected output Answered0 votes 7 comments
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GenomicsDBImport error from # fields in AS_UNIQ_ALT_READ_COUNT Answered0 votes 3 comments
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DetermineGermlineContigPloidy error with exome germline data Answered0 votes 5 comments
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hs37d5 genome in the GATK bundle Answered0 votes 3 comments
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gatk GenotypeGVCFs produced an error Answered0 votes 7 comments
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Error while running CreateReadCountPanelOfNormals Answered-1 votes 4 comments
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GATK v4.2.4.0 VariantAnnotator running too slow Answered0 votes 21 comments
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selectvariants error when consolidating GVCFs Answered0 votes 3 comments
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FilterVariantTranches Error: 'no variants with INFO score key "CNN_2D"' Answered1 vote 7 comments
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Haplotypecaller yields none mutation records Answered0 votes 1 comment
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Error using FindBreakpointEvidenceSpark Answered0 votes 7 comments
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Combine GVCFs Answered0 votes 6 comments
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Values for InbreedingCoeff annotation not detected for ANY training variant Answered0 votes 6 comments