General Discussion
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Need clarifications on the GVCF format0 votes 0 comments
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DRAGMAP and Mutect?0 votes 1 comment
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gCNV steps taking too long on server vs desktop pc.0 votes 0 comments
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Somatic Hotspot mutation is filtered although evident with IGV0 votes 1 comment
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Error running gatk HaplotypeCaller with allele specific annotations Answered0 votes 1 comment
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PathSeqBuildReferenceTaxonomy Answered0 votes 3 comments
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CalculateContamination differs much in single and paired mode0 votes 11 comments
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pooled experiment means Answered0 votes 4 comments
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GATK GenotypeGVCFs --sample-ploidy Answered0 votes 2 comments
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What code changes would I need to make to enable direct reads from S3?0 votes 1 comment
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CreateSequenceDictionary and BWASpark 'file already exists' error Answered0 votes 3 comments
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ScatterIntervalList error message when running DRAGEN-GATK on HPC0 votes 1 comment
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GATK ApplyBQSR error Answered0 votes 1 comment
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bait_set_name in WGS DRAGEN-GATK pipeline Answered0 votes 1 comment
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Missing files in GATK resource bundle hg38 Answered0 votes 1 comment
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mutect2 turm-only pipeline missing low AF Answered0 votes 2 comments
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GATK-DRAGEN standalone pipeline? Answered0 votes 3 comments
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GenomicDBimport error Answered0 votes 5 comments
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Variant calling for matched samples Answered0 votes 3 comments
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What's wrong with my GATK HaplotypeCaller result without ALT Answered0 votes 1 comment
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GATK Haplotypecaller - different variant calls from bam generated using converted fastq Answered0 votes 3 comments
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Single sample VCF file showed many alternate alleles Answered0 votes 2 comments
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Queey regarding Read group effect on Haplotype caller and Pipeline steps Answered0 votes 6 comments
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No output from PathSeqFilterSpark0 votes 1 comment
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How to filter out low quality bases?0 votes 0 comments
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there is zero ALT reads but the Allele Frequency is not zero Answered0 votes 2 comments
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Is it recommended that we limit Mutect2 analysis to target regions if analyzing whole exome data? Answered0 votes 2 comments
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A plan to release the log4j version update? Answered0 votes 3 comments
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Create panel of normals (PoN) with only one normal sample or using the public PoN? Answered0 votes 2 comments