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数据与复现
BI
bio-gatk-variant-calling
维护者 FreedomIntelligence · 最近更新 2026年4月1日
bio-gatk-variant-calling：Variant calling ，支持 GATK HaplotypeCaller following best practices。 Covers germline SNP/indel calling，GVCF workflow ，用于 cohorts，joint genotyping，、 variant quality score recalibration (VQSR)。 适合在calling variants ，支持 GATK HaplotypeCaller时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-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
Single-Sample Calling
Goal: Call germline SNPs and indels from a single sample using HaplotypeCaller.
Approach: Run local de novo assembly of haplotypes in active regions to detect variants with optional annotation enrichment.
"Call variants from my BAM file using GATK" → Perform local haplotype assembly and genotyping on aligned reads using HaplotypeCaller.
GVCF Workflow (Recommended for Cohorts)
Goal: Enable joint genotyping across a cohort by generating per-sample genomic VCFs.
Approach: Call each sample in GVCF mode (-ERC GVCF), combine into a GenomicsDB or merged GVCF, then jointly genotype.
The GVCF workflow enables joint genotyping across samples for better variant calls.
适用场景
- 适合在calling variants ，支持 GATK HaplotypeCaller时使用。
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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