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joint-calling

Maintainer FreedomIntelligence · Last updated April 1, 2026

joint-calling.

OpenClawNanoClawAnalysisReproductionjoint-callingopenclaw medical skillsadditional scientific toolsjoint

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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

Source Doc

Excerpt From SKILL.md

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