Germline
Forum thread to discuss GATK Germline tools
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Force genotype with specific reference-allele combinations0 votes 8 comments
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PostprocessGermlineCNVCalls does not report QUAL in output vcf for cnv0 votes 5 comments
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gatk 4.2.6.1 BaseRecalibrator cycle covariate0 votes 4 comments
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Bins for dp_hist_all_bin_freq0 votes 2 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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GenotypeGVCFs 'Cannot decompress with GZIP: inflate error: Z_DATA_ERROR'0 votes 1 comment
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Picard CollectWGSMetrics vs QualiMap vs samtools stats0 votes 1 comment
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Call copy number variants with GermlineCNVCaller0 votes 25 comments
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ValueError in DetermineGermlineContigPloidy0 votes 2 comments
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GetPileupSummaries all outputs zero0 votes 4 comments
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0 AD/DP for called variant in HaplotypeCaller0 votes 1 comment
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GATKgCNV References For Hg19 and Hg380 votes 7 comments
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--interval-padding range differs called variants0 votes 1 comment
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Trio de novo variants calling pipeline confuse1 vote 4 comments