流程自动化科研基础设施FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

joint-calling

维护者 FreedomIntelligence · 最近更新 2026年4月1日

joint-calling。

OpenClawNanoClaw分析处理复现实验joint-callingopenclaw medical skillsadditional scientific toolsjoint

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/joint-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

2 min

核心说明

Call variants jointly across multiple samples ，用于 improved accuracy 、 consistent genotyping。
gatk HaplotypeCaller \ -R reference.fa \ -I sample1.bam \ -O sample1.g.vcf.gz \ -ERC GVCF。

原始文档

SKILL.md 摘录

Why Joint Calling?

Improved sensitivity - Leverage information across samples
Consistent genotyping - Same sites called across all samples
VQSR eligible - Requires cohort for machine learning filtering
Population analysis - Allele frequencies across cohort

With intervals (faster)

gatk HaplotypeCaller
-R reference.fa
-I sample1.bam
-O sample1.g.vcf.gz
-ERC GVCF
-L intervals.bed


## Process all samples

for bam in *.bam; do
    sample=$(basename $bam .bam)
    gatk HaplotypeCaller \
        -R reference.fa \
        -I $bam \
        -O ${sample}.g.vcf.gz \
        -ERC GVCF &
done
wait