Germline
Forum thread to discuss GATK Germline tools
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Germline CNV calling for bulk WGS data aligned to hs37d5_PhiX.fa0 votes 2 comments
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Java large integer formatting error in GnarlyGenotyper0 votes 7 comments
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FuncotatorDataSourceDownloader: Requester Pays0 votes 4 comments
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Error in GATK-SV joint-calling terra pipeline, 07-FilterBatchSites step0 votes 9 comments
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HaplotypeCaller's Underlying Statistical Model0 votes 1 comment
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HaplotypeCaller and SoftClipped bases0 votes 3 comments
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Spurios indel0 votes 1 comment
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VariantFiltration ReadPosRankSum & MQRankSum undefined0 votes 7 comments
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PostprocessGermlineCNVCalls returns error for sample_name.txt file0 votes 4 comments
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What happens with VariantRecalibrator when annotations are missing?0 votes 1 comment
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Error in GnarlyGenotyper (QUALapproxkey)0 votes 3 comments
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Hard filtering using using germline-resource0 votes 1 comment
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AssertionError: Some samples do not have read depth metadata0 votes 2 comments
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GATK ApplyBQSR failing1 vote 2 comments
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gvcf in Dragen mode and GenomicsDBImport0 votes 3 comments
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disabled all read filters but reads are still filtering0 votes 7 comments
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Problem with Germline CNV CollectReadCounts0 votes 7 comments
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Problem with DenoiseReadCounts0 votes 3 comments
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Implicit Assumption of Germline Short Variant Discovery0 votes 1 comment
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Assistance Required with DetermineGermlineContigPloidy in GATK 4.60 votes 5 comments
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The optimization step for ELBO update returned a NaN0 votes 11 comments
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gatk 4.2.6.1 BaseRecalibrator cycle covariate0 votes 4 comments
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PostprocessGermlineCNVCalls does not report QUAL in output vcf for cnv0 votes 5 comments
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Force genotype with specific reference-allele combinations0 votes 8 comments