home/categories/bioinformatics/freedomintelligence-openclaw-medical-skills-skills-bio-gatk-variant-calling-skill-md
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bio-gatk-variant-calling
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
maintainer
FreedomIntelligence
Updated 3/8/2026
Stars
1987
Forks
270
quick start
Installation and usage
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
Installation
$ install --globalskills.sh
Usage
Once installed, you can use this skill by running the following command in your terminal:
skills use bio-gatk-variant-calling