Germline
Forum thread to discuss GATK Germline tools
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Caused by: java.util.zip.ZipException: Not in GZIP format0 votes 1 comment
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Error running DenoiseReadCounts on arm64 processor Answered0 votes 5 comments
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Variant not called with HaplotypeCaller0 votes 12 comments
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Haplotypecaller : variant calling not seen in bamout alignments Answered0 votes 14 comments
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Haplotypecaller too long ? Answered0 votes 5 comments
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sample DP(read coverage) is large but the genotype is ./. Answered0 votes 5 comments
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can't generate .segment.vcf.gz when use PostprocessGermlineCNVCalls Answered0 votes 1 comment
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fail to execute GermlineCNVCaller Answered0 votes 1 comment
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ApplyVQSR AS_FilterStatus=VQSRTrancheSNPXXXXtoXXXX but variant still passes FILTER Answered0 votes 3 comments
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fail to execute DetermineGermlineContigPloidy Answered0 votes 1 comment
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BaseRecalibrator java.lang.NullPointerException Answered0 votes 3 comments
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WholeGenomeGermlineSingleSample, hg38 reference, missing contamination resources Answered0 votes 1 comment
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Artificial haplotype generates a new variant for a homozygous site0 votes 3 comments
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gatk CNNScoreVariants is alway Loading libgkl_utils.so Answered0 votes 5 comments
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GenomicsDBImport output "unmapped" in ProgressMeter and running very slow with WGS data of large sample size Answered0 votes 6 comments
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genomicDBimport ERROR: java.lang.NumberFormatException: For input string Answered0 votes 8 comments
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Degenerate bases in 1000 genomes fasta reference Answered0 votes 5 comments
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Bug in GATK4 variant calling followed by CalculateGenotypePosteriors Answered0 votes 14 comments
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HaplotypeCallerSpark Answered0 votes 1 comment
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BQSR Pipeline Spark0 votes 3 comments
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Haplotype caller fails to run (GATK 4.1.8.0 and GATK 4.2.0.0) Answered0 votes 6 comments
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CNNScoreVariants/ValueError/version 4.1.9.0 and 4.2.0.0 Planned0 votes 2 comments
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A USER ERROR has occurred: Badly formed genome unclippedLoc0 votes 3 comments
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CombineGVCF on chrX and chrY hg38 running for ever0 votes 15 comments
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Using GenotypeGVCFs with GenomicsDB0 votes 2 comments
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HaplotypeCaller 4.2.0.0 new error0 votes 5 comments
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SetNmMdAndUqTags is mandatory?0 votes 5 comments
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HaplotypeCaller not running or producing error code Answered0 votes 1 comment