General Discussion
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pcr-free libraries and duplicate removal0 votes 0 comments
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Trouble installing GATK via conda – any tips?0 votes 0 comments
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Has anyone used GATK4 for RNA-seq analysis?0 votes 0 comments
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VCF + gVCF0 votes 1 comment
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GenotypeGVCF: How can I get AF for each sample?1 vote 3 comments
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forgot to set --is-host-aligned on aligned BAM0 votes 1 comment
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HS_LIBRARY_SIZE doesn't calculate when running CollectHsMetrics0 votes 1 comment
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Joint call a subset of samples from GenomicsDB datastore0 votes 1 comment
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SNPs and INDELs from RNA-seq mapping to introns0 votes 1 comment
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Finding tumor-specific variants0 votes 1 comment
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Is MarkDuplicates useful for GBS data?0 votes 1 comment
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GATK HaplotypeCaller Query0 votes 4 comments
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Mutect2 Somatic Variant Calling for WES Data from Different Library Versions0 votes 3 comments
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Merge libraries before IndelRealignment0 votes 1 comment
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HaplotypeCaller Not Detecting Variants0 votes 2 comments
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Allele frequencies missing in germline resource for mus musculus0 votes 2 comments
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Whether Mutect2 discards alignments in variant calling0 votes 1 comment
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Understanding how GATK handles sequence coverage normalisation0 votes 1 comment
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Missing DUP genotypes from Germline CNV calling output0 votes 1 comment
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GenomicsDBImport ended without results0 votes 3 comments
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Mutect2 tumor-only mode without normal match or germline resources0 votes 1 comment
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Picard issue0 votes 5 comments
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Lanes from same sample show very discordant called variant results.0 votes 15 comments
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Negative number in the output file of CompareSAMs0 votes 3 comments
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GATK GRCh38 Reference0 votes 1 comment