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GATK-SV — Broad Institute WDL pipeline for end-to-end structural variant (SV) discovery, genotyping, and filtering from short-read whole-genome sequencing. Detects deletions, duplications, inversions,
Use with AI
Install the MCP server or CLI to instantly fetch GATK-SV documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gatk-sv
Tools and workflows for accessing, querying, and analyzing data from the 1000 Genomes Project (1KGP) — the largest public catalog of human genetic variation with whole-genome sequences from 3,202 indi
2 shared topics • 2 shared operations
GATK VQSR (Variant Quality Score Recalibration) — machine learning-based variant filtering for GATK Best Practices germline pipelines. Trains a Gaussian mixture model on truth/training resource datase
2 shared topics • 2 shared operations
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
2 shared topics • 2 shared operations
SnpSift -- Java-based toolset for filtering, annotating, and manipulating annotated VCF files from SnpEff or other variant callers. Provides expression-based filtering (filter), database annotation wi
2 shared topics • 2 shared operations
Strelka2 — fast and accurate small variant caller for germline and somatic analysis. Detects SNVs and indels (up to ~49 bp) from mapped paired-end sequencing reads with tiered haplotype modeling, adap
2 shared topics • 2 shared operations