General Discussion
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Mutect2 produces empty VCF file but job doesn't fail0 votes 1 comment
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Individual bwa, dict files, and tax files for bacteria, fungi, and viruses.0 votes 0 comments
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GenotypeGVCF by intervals emitted ALT allele at a missing site0 votes 8 comments
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FilterMutectCalls - unfiltered.vcf.stats file not found0 votes 2 comments
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DRAGEN-GATK and joint genotyping0 votes 3 comments
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Mutect2 MBQ correction of pcr overlapping in UMI reads0 votes 1 comment
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How long will gatk PathSeqPipelineSpark run？0 votes 0 comments
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GATK suddenly exit without error message0 votes 1 comment
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T2T0 votes 3 comments
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Mutect2 heteroplasmy sensitivity0 votes 1 comment
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CNNScoreVariants, python timeout error occurred0 votes 7 comments
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MergeBamAlignment Error - java.lang.IllegalArgumentException Answered0 votes 8 comments
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AnalyzeSaturationMutagenesis behavior with disjoint pairs0 votes 6 comments
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cutting down on db or fa file based off of .txt results in pathseqspark0 votes 1 comment
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GATK 4.2.5.0 = which version of Java or other requirements? Answered0 votes 2 comments
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Reinstall GATK40 votes 1 comment
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Question regarding funcotator datasets0 votes 2 comments
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A USER ERROR has occurred: Invalid argument 'hg38.fa'.0 votes 3 comments
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gtf file for hg38_v0_chrM_Homo_sapiens_assembly38.chrM.fasta0 votes 1 comment
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What's the right order of Mitochondrial pipeline0 votes 5 comments
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Novaseq X - OPTICAL_DUPLICATE_PIXEL_DISTANCE0 votes 1 comment
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GenomicsDBImport for joint genotyping Answered0 votes 3 comments
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ExtractIlluminaBarcodes not using more than 1 cpu0 votes 11 comments
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Mitochondrial LiftoverVcf0 votes 2 comments
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How to find unique variants among individual-level VCF files?0 votes 3 comments
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Pipeline for germline, short variant discovery in targeted sequencing data0 votes 3 comments
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Picard CollectInsertSizeMetrics 3.1.0 doesn't find R0 votes 4 comments