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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Speeding up GenotypeGVCFS? GATK4 Answered0 votes 17 comments
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GenomicsDBImport very slow on genome with many contigs Answered1 vote 17 comments
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Error Creatting Dictionary for genome Answered0 votes 16 comments
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emit-ref-confidence error Answered0 votes 15 comments
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Issues while running GenotypeGVCFs Answered0 votes 11 comments
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StrandBiasBySample SB in vcf Answered0 votes 10 comments
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GATK GenotypeGVCFs stuck on starting traversal Answered1 vote 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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VariantFiltration Answered0 votes 7 comments
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VQSR: how is insufficient variance inferred for annotations? Answered0 votes 7 comments
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Haplotype caller error; java.lang.IllegalStateException: Graph must have ref source and sink vertices Answered0 votes 6 comments
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VariantEval does not work or something wrong with my ref genome and dbsnps? Answered0 votes 5 comments
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ArtificialHaplotypeRG makes variant heterozygous Answered0 votes 5 comments
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HaplotypeCaller with additional annotation? Answered0 votes 5 comments
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GenotypeGVCF: How can I know which sample falied in joint genotyping? Answered0 votes 5 comments
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How do I call germline variants with multiple samples -non human? Answered0 votes 5 comments
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VariantFiltration undefined variable Answered0 votes 5 comments
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known-sites for Felis_catus_9.0 (GCA_000181335.4) Answered0 votes 4 comments
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GenotypeGvcf tetraploids as diploids Answered0 votes 4 comments
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FindBreakpointEvidenceSpark sudden shutdown Answered0 votes 4 comments
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Query regarding CombineGVCFs Answered0 votes 4 comments
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Receiving zero variants processed after HaplotypeCaller and Select Variants Answered0 votes 4 comments
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REAL Variant not called by HaplotypeCaller Answered1 vote 4 comments
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emit-ref-confidence error Answered0 votes 3 comments
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Inconsistent variant call in some pool-seq samples Answered0 votes 3 comments
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gatk MarkDuplicatesSpark exits without error message Answered0 votes 3 comments
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Some <NON_REF> alleles remain after GenotypeGVCFs when using --include-non-variant-sites Answered0 votes 3 comments