Non-Human
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REAL Variant not called by HaplotypeCaller Answered1 vote 4 comments
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FixMateInformation does not solve ERROR:MATE_NOT_FOUND1 vote 7 comments
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GATK-HaplotypeCaller results generate records with read depth of zero?1 vote 2 comments
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HaplotypeCaller for denovo RNAseq output1 vote 3 comments
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GenomicsDBImport very slow on genome with many contigs Answered1 vote 17 comments
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Analy1 vote 3 comments
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HaplotypeCaller does not recognize the RefSeqfile1 vote 2 comments
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GATK for Rnor6 - Funcotator error0 votes 0 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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All intervals were filtered in Filterintervals0 votes 11 comments
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FindBreakpointEvidenceSpark sudden shutdown Answered0 votes 4 comments
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emit-ref-confidence error Answered0 votes 3 comments
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gatk4-4.2.4.0-0 Fixmate Error Answered0 votes 2 comments
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GATK HaplotypeCaller disable filter -DF with the error in positional argument value Answered0 votes 1 comment
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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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ValidateSamFile Error Answered0 votes 1 comment
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Query regarding CombineGVCFs Answered0 votes 4 comments
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Inconsistent variant call in some pool-seq samples Answered0 votes 3 comments
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GatherVcfs - File number limit?0 votes 3 comments
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GATK GenotypeGVCFs stuck on starting traversal Answered0 votes 7 comments
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How do iquery VCF for specific variants by CHROM and POS0 votes 3 comments
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No downsampling with max-reads-per-alignment-start0 votes 3 comments
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ArtificialHaplotypeRG makes variant heterozygous Answered0 votes 5 comments
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Preform variant calling on 50 bp SE rna-seq data0 votes 4 comments
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gatk MarkDuplicatesSpark exits without error message Answered0 votes 3 comments
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HaplotypeCaller with additional annotation? Answered0 votes 5 comments
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Issues while running GenotypeGVCFs Answered0 votes 11 comments