Germline
Forum thread to discuss GATK Germline tools
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Error while running CreateReadCountPanelOfNormals0 votes 11 comments
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VariantFiltration ReadPosRankSum & MQRankSum undefined0 votes 3 comments
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Calling variants on chromosome Y1 vote 5 comments
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unable to create contig_ploidy_model1 vote 3 comments
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(How to) Call common and rare germline copy number variants - which bamfile0 votes 6 comments
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DetermineGermlineContigPloidy error0 votes 1 comment
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Problem with Germline CNV CollectReadCounts0 votes 3 comments
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Convert combineGVCF result to GenomicsDB [Repost] Answered1 vote 14 comments
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pcr-indel-model and PCR-free: Best Practise pipelines vs tool documentation0 votes 2 comments
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problems in joint-calling0 votes 5 comments
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HaplotypeCaller: data generated from amplicon sequencing0 votes 2 comments
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Error while running GenotypeGVCFs0 votes 1 comment
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CNNScoreVariants in conda environment: CXXABI_1.3.11 not found0 votes 1 comment
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gatk4-genome-processing-pipeline Implementation Issues0 votes 2 comments
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Error running DetermineGermlineContigPloidy0 votes 2 comments
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GATK Germline CNV strange error0 votes 5 comments
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DetermineGermlineContigPloidy error0 votes 4 comments
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ExcessHet value is -0.00000 votes 2 comments
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BAM file and VCF file showing different results0 votes 11 comments
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Haplotypecaller usage (version decrepancy)0 votes 2 comments
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Trio calling with GATK, LowGQ0 votes 1 comment
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Cannot access GATK resource bundle link0 votes 1 comment
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Phasing in joint calls0 votes 3 comments
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FilterVariantTranches User error0 votes 4 comments
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genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file Answered0 votes 7 comments
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GATK Funcotator and GATK VariantFiltration0 votes 15 comments