Non-Human
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GenotypeGVCFs stalls while using --all-sites Answered0 votes 37 comments
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gatk HaplotypeCaller gives me an empty vcf Answered0 votes 18 comments
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GenomicsDBimport not importing all the batches0 votes 18 comments
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GenomicsDBImport very slow on genome with many contigs Answered1 vote 17 comments
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Speeding up GenotypeGVCFS? GATK4 Answered0 votes 16 comments
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emit-ref-confidence error Answered0 votes 15 comments
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Haplotypecaller produce unfinished vcf but no idx (no error)0 votes 13 comments
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Error Creatting Dictionary for genome Answered0 votes 12 comments
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All intervals were filtered in Filterintervals0 votes 11 comments
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Issues while running GenotypeGVCFs Answered0 votes 11 comments
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Provider "genedb" not found when using SelectVariants & GenomicsDBImport0 votes 11 comments
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StrandBiasBySample SB in vcf Answered0 votes 10 comments
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Getting an error with genomicsdbimport0 votes 9 comments
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Unphased homozyous sites between phased heterozygous sites0 votes 9 comments
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java.lang.IllegalStateException in GenotypeGVCFs after GenomicsDBImport, GATK 4.2.6.1 Answered0 votes 8 comments
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GenotypeGvcfs has formatting issues in both v4.1.6.0 as v4.1.7.00 votes 8 comments
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StrandBiasBySample error Haplotypecaller0 votes 8 comments
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bqsr output issue0 votes 8 comments
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HaplotypeCaller local Assembly0 votes 8 comments
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Empty vcf after GenotypeVCFs when combining already genotyped samples0 votes 8 comments
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Error running HaplotypeCaller?0 votes 8 comments
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GATK GenotypeGVCFs stuck on starting traversal Answered0 votes 7 comments
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VariantFiltration Answered0 votes 7 comments
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Keras error in CNNScoreVariants0 votes 7 comments
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VQSR: how is insufficient variance inferred for annotations? Answered0 votes 7 comments
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FixMateInformation does not solve ERROR:MATE_NOT_FOUND1 vote 7 comments
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Missing MQ scores in gvcf0 votes 7 comments
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HaplotypeCaller for haploid genome0 votes 7 comments