The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy …

2024年7月20日 · Basic syntax is gatk [--java-options "-Xmx4G"] ToolName [GATK args]; full details here. Use the Terra workspaces to test the pipelines and learn what each tool does. If …

GATK Best Practices for Structural Variation Discovery on Single Samples GATK-SV is a structural variation discovery pipeline for Illumina short-read ... Mitochondrial short variant …

2024年6月25日 · Funcotator is a functional annotation tool in the core GATK toolset and was designed to handle both somatic and germline use cases. Funcotator reads in a VCF file, …

2021年9月1日 · If you’ve been following our modest little blog, you know that we’ve been preparing to transfer the GATK website and forum to a new home. Well, moving day has finally …

2025年2月5日 · A highly recommended whitepaper detailing the methods is in the gatk GitHub repository's docs/CNV directory. For pipelined workflows, see the gatk GitHub repository's …

2024年7月3日 · The gatk-launch wrapper script requires Python 2.6 or greater. Some of the newer tools and workflows require Python 3.6.2 along with a set of additional Python …

Tool documentation for GATK release 4.6.1.0 * Tool Documentation Index ... AccumulateQualityYieldMetrics (Picard) Combines multiple QualityYieldMetrics files into a …

A GATK Report file with many tables: The list of arguments; The quantized qualities table; The recalibration table by read group; The recalibration table by quality score; The recalibration …

2014年8月20日 · The GATK requires several read group fields to be present in input files and will fail with errors if this requirement is not satisfied. See this article for common problems related …