Germline
Forum thread to discuss GATK Germline tools
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erro in VQSR (WGS)0 votes 1 comment
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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 5 comments
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Unable to trim uncertain bases without flow order information0 votes 0 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
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gCNV SVLEN question0 votes 4 comments
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CombineVariants Doesnt produce output0 votes 1 comment
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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
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Potential guidance on GenomeSTRiP CNV discovery on Anvil Terra app1 vote 5 comments
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workspace.haplotype_database_b370 votes 1 comment
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BaseRecalibrator java.lang.NullPointerException0 votes 1 comment
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GATK GenotypeGVCFs changes HET to REF_ALT0 votes 0 comments
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BQSR and VQSR resource sequences0 votes 1 comment
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CNNScoreVariants has no output and print java.lang.NullPointerException0 votes 7 comments
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GermlineCNVCaller prefix string too short0 votes 9 comments