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GATK4 — Genome Analysis Toolkit for germline and somatic short variant discovery (SNPs and indels). Industry-standard caller providing HaplotypeCaller for germline, Mutect2 for somatic, plus Base Qual
Use with AI
Install the MCP server or CLI to instantly fetch GATK4 (Genome Analysis Toolkit) documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gatk4
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3 shared topics • 2 shared operations
Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.
3 shared topics • 1 shared operation
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3 shared topics • 1 shared operation
Java command-line tools from the Broad Institute for manipulating high-throughput sequencing data and formats including BAM, CRAM, and VCF.
3 shared topics • 1 shared operation
WDL/Cromwell — Workflow Description Language (WDL) authoring and Cromwell execution engine for reproducible bioinformatics pipelines. WDL defines portable, composable workflows using task/workflow blo
3 shared topics • 1 shared operation