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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GATK GenomicsDBimport Error with TileDB Answered1 vote 2 comments
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Can't generate ploidy-calls directory and ploidy-calls/SAMPLE_0 when use DetermineGermlineContigPloidy Answered0 votes 2 comments
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Before using GATK, do I need to use short-read error correction tools such as RACER or HiTEC? Answered0 votes 1 comment
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mtDNA calling problems Answered0 votes 3 comments
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Extracting gene segments that is in anti-sense/negative strand0 votes 1 comment
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Why the genedb needs 'appropriate extension' in GenotypeGVCFs? Answered0 votes 3 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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GermlineCNVCaller in CASE mode using too many CPU for denoising Answered0 votes 4 comments
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variant calling: dict and indexing0 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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GATK gCNV Calling pipeline error0 votes 0 comments
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Missing RawGtCount annoation from GenotypeGVCF output0 votes 19 comments
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Unable to trim uncertain bases without flow order information Answered0 votes 7 comments
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Howto call germline SNPs from reads with MAPQ=00 votes 0 comments
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GenotypeGVCFs : VariantQueryProcessorException0 votes 5 comments
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Varinat PASS given Genotype quality = 00 votes 2 comments
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JointGenotyping.ImportGvcfs terminates without an active exception0 votes 4 comments
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HaplotypeCaller interval list0 votes 1 comment
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Jointgenotyping Genomicsdbimport failed for no obvious reasons1 vote 1 comment