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GATK Best Practices Mitochondrial Analysis1 vote 29 comments
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Genome STRiP CNVDiscovery pipeline error0 votes 27 comments
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ValidateSamFile: New error after running BQSR0 votes 19 comments
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How to run GenotypeConcordance0 votes 19 comments
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Problem Installing GATK python environment - SOLUTION POSTED! Featured1 vote 17 comments
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filterSamReads stdout format error0 votes 15 comments
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Fatal error occuring during GATK4 PathSeqPipeline tool run0 votes 15 comments
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MarkDuplicatesSparks not removing some duplicates?0 votes 15 comments
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Setting SPARK resources when using the gatk release version0 votes 15 comments
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Broken: conda env create -n gatk -f gatkcondaenv.yml0 votes 15 comments
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Error running FilterMutectCalls: alpha must be greater than 0 but got NaN0 votes 13 comments
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DepthofCoverage GATK4.1.7.0 -gene-list0 votes 13 comments
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Any automatic downloadable gatk3?2 votes 13 comments
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Error in SplitNCigarReads0 votes 11 comments
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FilterByOrientationBias vanished in 4.1.6.00 votes 11 comments
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CNNScoreVariants carshes with java.lang.NullPointerException Answered1 vote 11 comments
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Merge different individual VCF0 votes 10 comments
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Panel of Normals Documentation0 votes 10 comments
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HaplotypeCaller complains (in 2 different ways) about sample-name0 votes 10 comments
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GenomeStrip SVPreprocess works with for a chromosome region; but fail for whole genome Answered0 votes 10 comments
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Clear missing variant from HaplotypeCaller0 votes 9 comments
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--tmp-dir option user error0 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