New User Advice
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Mutect2 somatic mutation calling for plant0 votes 2 comments
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Running best practices workflow step-by-step in command line1 vote 5 comments
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Empty intersection error when applying intervals Answered0 votes 3 comments
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GQ in jointly genotyped samples Answered0 votes 1 comment
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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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Counld I use bam files from HISAT2 to call snp/indels? Answered0 votes 2 comments
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Help with WDL workflow for mutec2? Answered0 votes 5 comments
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Problems with FastQtoSAM Answered0 votes 3 comments
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Combining mplileup and haplotypeCaller calls Answered0 votes 2 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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gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) Answered0 votes 3 comments
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picard CollectAlignmentSummaryMetrics required arguments format Answered0 votes 1 comment
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VQSR dataset preparation Answered0 votes 2 comments
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Sensitive Copy Ratio Pipeline compatibility with tool "mergeLevels"0 votes 1 comment
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ValiidateSamFile Error: Mate not found Answered0 votes 9 comments
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Somatic Structure Variation on exome-seq data0 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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Mutect2 with and without UMI information Answered0 votes 1 comment
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Distinct allele frequency patters by HaplotypeCaller and Mutect2 for the same sample Answered0 votes 1 comment
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Why doesn't haplotypecaller use PON?0 votes 1 comment
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Picard CheckIlluminaDirectory - Issue with file/folder structure?0 votes 1 comment
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Updating Picard to latest version Answered0 votes 1 comment
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Failed on the variants calling with low quality pacbio seq Answered0 votes 1 comment
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Invalid or corrupt jar file Answered0 votes 3 comments
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DP for each variant bulk is skewed towards 50 and multiples of 500 votes 7 comments
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How do I pool normal samples in mutect2? Answered0 votes 1 comment
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At which stage family genotype posterior recommened in germline discovery best practice? Answered0 votes 1 comment
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Scatter / Gather for BaseRecalibrator on a single human WES dataset0 votes 2 comments