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GATK Mutect2 counts the alternate base twice in overlapping paired reads0 votes 5 comments
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CombineGVCFs vs GenomicsDBImport for target sequencing data0 votes 1 comment
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FastqToSam error when using paired reads0 votes 1 comment
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VQSR SNP ggplot error.0 votes 2 comments
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genotypeGVCFs won't use more than 2G no matter how much memory I give it...0 votes 3 comments
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VariantAnnotator not recognising QD annotations0 votes 5 comments
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GenomicsDBImport only going through the first chromosome when given a list0 votes 3 comments
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Funcotator problem0 votes 1 comment
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Funcotator missing ClinVar annotations0 votes 3 comments
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BWASpark error while using local cluster0 votes 1 comment
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Open source software for reprocessing WGS samples run by GATK to Dragen0 votes 1 comment
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Troubleshooting VCF Output Truncation Issue during GATK CombineGVCFs Process0 votes 5 comments
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error in mitochondria pipeline0 votes 6 comments
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Output in SortSam was not generated0 votes 2 comments
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Mutect 2 on mitochondria DNA variant discovery0 votes 26 comments
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Cromwell GCP Batch launch errors0 votes 1 comment
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Setting up Cromwell on AWS0 votes 1 comment
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LeftAlignIndels not recognizing input/reference/output strings0 votes 4 comments
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Link checking for the GATK documentation0 votes 1 comment
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MakeSitesOnlyVCF deletes the most of the variants from cohort vcf0 votes 1 comment
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GATK haplotype caller struggling to find variant that exists0 votes 3 comments
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GenotypeGVCFs hangs at GenomicsDBLibLoader0 votes 3 comments
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Muect2 is running till Chr1 and there no stats file0 votes 1 comment
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SplitNCigar reads tool is not running0 votes 1 comment
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ASEReadCounter output wrong number of coverage0 votes 1 comment
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Error when building an image using Dockerfile0 votes 2 comments
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Issue with GenotypegVCFS after Genomics DB import, building vs updating0 votes 6 comments