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SAIGE-GENE+ — gene-based and region-based rare variant association testing using mixed models. Extends SAIGE to aggregate rare variants (SKAT, Burden, SKAT-O) while controlling for population structur
Use with AI
Install the MCP server or CLI to instantly fetch SAIGE-GENE+ documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/saige-gene
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
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GATK (Genome Analysis Toolkit) — the industry-standard framework for variant discovery in high-throughput sequencing data. Covers the gatk command-line wrapper, Java/JVM tuning, resource bundle manage
2 shared topics • 2 shared operations
Nirvana — Clinical-grade genomic variant annotation tool by Illumina that processes VCF files and outputs structured JSON with transcript consequences, population frequencies, pathogenicity scores, an
2 shared topics • 2 shared operations
Sarek — nf-core Nextflow pipeline for germline and somatic variant calling from whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted sequencing data. Supports multiple variant cal
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