Germline
Forum thread to discuss GATK Germline tools
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Wrong allosomal ploidies from DetermineGermlineContigPloidy.0 votes 0 comments
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HaplotypeCaller: missing INDELs0 votes 0 comments
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GenomicsDBImport vs CombineGVCFs0 votes 0 comments
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GenomicsDBImport error - non-standard non-IUPAC base0 votes 1 comment
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Extracting gene segments that is in anti-sense/negative strand0 votes 1 comment
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Missing RawGtCount annoation from GenotypeGVCF output0 votes 19 comments
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HaplotypeCaller - output g.vcf is not phased?0 votes 1 comment
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GATK HaplotypeCaller results in empty vcf0 votes 1 comment
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Has too many alleles in the combined VCF record0 votes 1 comment
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FastaAlternateReferenceMaker creating chimera0 votes 1 comment
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variant calling: dict and indexing0 votes 1 comment
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GATK gCNV Calling pipeline error0 votes 0 comments
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GenotypeGVCFs : VariantQueryProcessorException0 votes 5 comments
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HaplotypeCaller interval list0 votes 1 comment
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Howto call germline SNPs from reads with MAPQ=00 votes 0 comments
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Varinat PASS given Genotype quality = 00 votes 2 comments
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humanG1Kv37 (b37) to hg38 liftover issues0 votes 6 comments
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JointGenotyping.ImportGvcfs terminates without an active exception0 votes 4 comments
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gCNV SVLEN question0 votes 4 comments
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Jointgenotyping Genomicsdbimport failed for no obvious reasons1 vote 1 comment
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CombineVariants Doesnt produce output0 votes 1 comment
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VariantFiltration ReadPosRankSum & MQRankSum undefined0 votes 5 comments
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Ambiguity in Germline short variant best practices0 votes 1 comment
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python exited with 135 in germlinecnvcaller0 votes 5 comments