Non-Human
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GQ=0 upstream of regions with no mapped reads0 votes 4 comments
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HaplotypeCaller can't input the known variant from pooled samples0 votes 2 comments
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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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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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All intervals were filtered in Filterintervals0 votes 11 comments
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GatherVcfs - File number limit?0 votes 3 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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Preform variant calling on 50 bp SE rna-seq data0 votes 4 comments
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GenotypeGVCF too many genotypes1 vote 1 comment
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Unexpected SOR value changes0 votes 1 comment