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Clear missing variant from HaplotypeCaller0 votes 9 comments
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Genomestrip cannot find --ploidyMapFile0 votes 9 comments
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Recal file with malformed header0 votes 9 comments
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GenotypeGVCFs: java.lang.NullPointerException0 votes 9 comments
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MarkDuplicatesSpark crash1 vote 9 comments
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Can't explain the number of reads FilterSamReads outputs Answered0 votes 8 comments
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GermlineCNVCaller edge case?0 votes 8 comments
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IlluminaBasecallsToSam: How do I specify one unique RGID per output uBAM?0 votes 8 comments
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GenomicsDBImport running out of memory?0 votes 8 comments
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Error in running SplitNCigarReads - htsjdk.samtools.util.RuntimeIOException Answered0 votes 8 comments
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SelectVariants v4.1.6.0 doesn't select the variants as expected Answered0 votes 8 comments
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newbie question: how to split a genome bam file by using picard0 votes 8 comments
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Unable to replicate the spanning deletions documentation0 votes 8 comments
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GenomeSTRiP ReciprocalOverlapAnnotator Annotation track not sorted0 votes 8 comments
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AS_MQRanksum craches R script VQSR0 votes 8 comments
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Contamination calculation on single file don't detect contaminated samples Answered0 votes 7 comments
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DepthOfCoverage with -gene-list and readgroup as --partition-type options Answered0 votes 7 comments
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ApplyBQSR no positional argument is defined for this tool Answered0 votes 7 comments
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Comparison between ReadsPipelineSpark and MarkDuplicates0 votes 7 comments
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Resource bundle error download0 votes 7 comments
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Empty VCF file from Mutect2 v. GATK 4.1.6.0 in tumor only mode0 votes 7 comments
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error in GATK mitochondria pipeline0 votes 7 comments
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run SVPreprocess and SVGenotyper for each sample0 votes 7 comments
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Read Group: ID for split files of multiple samples on multiple lanes0 votes 7 comments
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HaplotypeCaller bam file path not recognized0 votes 7 comments
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ValidateSamFile behavior1 vote 7 comments
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CNNScoreVariants Issues with environment and Java version Answered0 votes 6 comments