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gatk-variant-calling
维护者 FreedomIntelligence · 最近更新 2026年4月1日
gatk-variant-calling.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/gatk-variant-calling
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- GATK HaplotypeCaller是一个gold standard ，用于 germline variant calling. This skill covers GATK Best Practices workflow。
- gatk GenomicsDBImport \ --genomicsdb-workspace-path genomicsdb \ --sample-name-map sample_map.txt \ -L intervals.interval_list。
原始文档
SKILL.md 摘录
Prerequisites
BAM files should be preprocessed:
- Mark duplicates
- Base quality score recalibration (BQSR) - optional but recommended
GVCF Workflow (Recommended for Cohorts)
The GVCF workflow enables joint genotyping across samples for better variant calls.
From GenomicsDB
gatk GenotypeGVCFs
-R reference.fa
-V gendb://genomicsdb
-O cohort.vcf.gz
适用场景
- Use gatk-variant-calling ，用于 genomics 、 bioinformatics workflows。
- Apply gatk-variant-calling to sequencing，variant，或 omics analysis tasks。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- variant-calling - bcftools alternative
- alignment-files - BAM preprocessing
- filtering-best-practices - Post-calling filtering
- variant-normalization - Normalize before annotation
- vep-snpeff-annotation - Annotate final calls
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