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Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
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npx skills add https://github.com/vimalinx/bio-agent --skill gatk-genotypegvcfsThe command stays on one line. Scroll horizontally to inspect it before copying.
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Showing SKILL.md
| name | gatk-genotypegvcfs |
| description | Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs. |
| disable-model-invocation | true |
| user-invocable | true |
gatk GenotypeGVCFs/home/vimalinx/miniforge3/envs/bio/bin/gatkgatk executable on PATH.gatk GenotypeGVCFs \
-R reference.fa \
-V cohort.g.vcf.gz \
-O cohort.joint.vcf.gz
gatk executable still has to exist for real execution.Based on SOC occupation classification
