Germline
Forum thread to discuss GATK Germline tools
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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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AssertionError: Some samples do not have read depth metadata0 votes 1 comment
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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
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Bins for dp_hist_all_bin_freq0 votes 2 comments
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Call copy number variants with GermlineCNVCaller0 votes 25 comments
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DetermineGermlineContigPloidy; Results does not contain chrY0 votes 8 comments
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GenotypeGVCFs issue when using --include-non-variant-sites parameter0 votes 2 comments
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gatk CombineGVCFs output contains only one Chr0 votes 8 comments
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Why Haplotypecaller gives me empty vcf (only the header) for all of my samples?0 votes 18 comments
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Can I continue to run Haplotypecaller when it is broken?1 vote 5 comments
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GenotypeGVCFs 'Cannot decompress with GZIP: inflate error: Z_DATA_ERROR'0 votes 1 comment