Germline
Forum thread to discuss GATK Germline tools
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VariantRecalibrator/ApplyVQSR SNP/INDEL separation does not work0 votes 8 comments
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Handling different ploidy for male samples during joint genotyping0 votes 1 comment
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Switching version of gatk during the workflow0 votes 1 comment
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Determine Contig Ploidy error_theano.gof.compilelock0 votes 1 comment
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Panel of normals for CNV exome analysis using WGS datasets0 votes 4 comments
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gCNV - Discrepancy in Results between Hg19 and Hg38 Cohort Models0 votes 3 comments
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Confirming variants0 votes 1 comment
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Problem with DenoiseReadCounts0 votes 1 comment
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Haplotypecaller Local Assembly Algorithm0 votes 3 comments
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depth of indel in a uncalled snp site0 votes 3 comments
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QUAL scores being returned as "." in output from CombineGVCFs0 votes 6 comments
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Canonical transcripts as determined by GATK0 votes 8 comments
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Physical Phasing oh alleles0 votes 1 comment
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GenomicsDBImport import both WES with WGS0 votes 1 comment
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Bug in VariantRecalibrator: Data not found0 votes 4 comments
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GATKgCNV Error: "Some contigs do not have ploidy priors"0 votes 32 comments
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Issue with RNA-seq Variant Calling Pipeline using GATK1 vote 3 comments
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HaplotyopeCaller SIGSEGV error in small region across multiple samples0 votes 4 comments
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HaplotypecallerSpark error0 votes 9 comments
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Error import gcnvkernel during GATK-SV cohort mode on local HPC0 votes 8 comments
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GermlineCNVCaller - I don't have a cohort, use public data?0 votes 4 comments
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CombineGVCFs vs GenomicsDBImport in 1000+ WES0 votes 1 comment
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GATK CNVs Ploidy Interpretation0 votes 1 comment
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Dragen-mode HaplotypeCaller - zygosities0 votes 1 comment