Germline
Forum thread to discuss GATK Germline tools
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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 17 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
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VariantRecalibrator error0 votes 1 comment
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Allele Specific vs normal annotations at non-multiallelic sites0 votes 1 comment
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CombineGVCFs outputs null genotypes for all samples0 votes 2 comments
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The imputation process in Germline short variant calling pipeline0 votes 2 comments
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[GATKv4.2] GenotypeGVCF emits non_ref sites and no AC,AN,AF0 votes 5 comments
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GenotypeGVCF not getting all samples1 vote 1 comment
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GenomicsDB and recalibration recommended for cohort of mixed exome0 votes 2 comments
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Error in calling with option --max-reads-per-alignment-start 00 votes 8 comments
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Best human reference genome chm13v2?1 vote 1 comment
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DetermineGermlineContigPloidy error0 votes 2 comments
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Exome Germline Single Sample with only BAM output0 votes 1 comment
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VQSR filtering differences0 votes 1 comment