New User Advice
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Where is my GATK4 ? Answered0 votes 1 comment
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Pileup output of GATK4 vs. GATK3 Answered0 votes 1 comment
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bash: gatk: command not found Answered0 votes 2 comments
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GATK GenomicsDBImport intervals Answered0 votes 19 comments
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rename sample in GVCF file Answered0 votes 3 comments
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GenotypeGVCFs produces bizarre mapping quality distribution0 votes 1 comment
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GATK Non-model organism variant call SNP site all MQ same value0 votes 1 comment
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MarkDuplicates analysis of large wheat chromosomes Answered0 votes 1 comment
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ApplyBQSR doesn't recognise my arguments? Answered0 votes 3 comments
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Exclude non variant sites Answered0 votes 1 comment
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Using GATK as a genotyper to genotype existing variants Answered0 votes 6 comments
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GATK4.0.3.0 - CombineGVCFs - Unexpected base in allele bases0 votes 4 comments
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Mutect2 somatic mutation calling for plant0 votes 2 comments
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Empty intersection error when applying intervals Answered0 votes 3 comments
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Script for using same GATK tool(s) on multiple sample files Answered0 votes 1 comment
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Creating dictionary for fasta reeference file Answered0 votes 1 comment
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GQ in jointly genotyped samples Answered0 votes 1 comment
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Combining mplileup and haplotypeCaller calls Answered0 votes 2 comments
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Help with WDL workflow for mutec2? Answered0 votes 5 comments
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looking for panel of normals and allele frequency for hg19 genome build Answered0 votes 1 comment
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picard CollectAlignmentSummaryMetrics required arguments format Answered0 votes 1 comment
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gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) Answered0 votes 3 comments
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ValiidateSamFile Error: Mate not found Answered0 votes 9 comments
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Mutect2 with and without UMI information Answered0 votes 1 comment
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7 things I learned while reprocessing my WGS data on Terra: part 10 votes 1 comment
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Picard CheckIlluminaDirectory - Issue with file/folder structure?0 votes 1 comment
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VQSR dataset preparation Answered0 votes 2 comments
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Updating Picard to latest version Answered0 votes 1 comment
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Distinct allele frequency patters by HaplotypeCaller and Mutect2 for the same sample Answered0 votes 1 comment