Non-Human
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HaplotypeCaller can't input the known variant from pooled samples0 votes 1 comment
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FastaAlternateReferenceMaker not replacing sites in fasta file0 votes 11 comments
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Annotate using funcotator0 votes 4 comments
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Question about bam format errors and handling large contigs0 votes 2 comments
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gatk-microbialmode.jar1 vote 4 comments
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known-sites for Felis_catus_9.0 (GCA_000181335.4) Answered0 votes 4 comments
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How to remove strand bias from a virus-derived signal-end NGS dataset0 votes 4 comments
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GATK HaplotypeCaller for non-model organism: gVCF output0 votes 0 comments
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Somatic Variant Calling for a non-model species not finding any variants0 votes 0 comments
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GenotypeGVCF error0 votes 0 comments
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The expected variants were not detected for pig RNA-seq by GATK1 vote 8 comments
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GatherVcfs to concatenate GVCFs0 votes 3 comments
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GenotypeGvcf tetraploids as diploids Answered0 votes 4 comments
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GATK for Rnor6 - Funcotator error Answered0 votes 1 comment
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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