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variant-annotation
95 / 100 · Low risk
Fine to try.
By mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- (GitHub) · other · 36 stars · scanned at commit fde6cd1
Works with any agent that supports SKILL.md skills.
Partially scanned — some files couldn't be read; we'll retry on the next scan
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 21 places.
Show 17 more
- Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 69
bcftools annotate -a regions.bed.gz -c CHROM,FROM,TO,INFO/REGION \ - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 82
bcftools annotate -x INFO/DP,INFO/MQ input.vcf.gz -Oz -o clean.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 89
bcftools annotate --set-id '%CHROM\_%POS\_%REF\_%ALT' input.vcf.gz -Oz -o with_ids.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 97
bcftools csq -f reference.fa -g genes.gff3.gz input.vcf.gz -Oz -o consequences.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 115
conda install -c bioconda ensembl-vep - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 122
vep -i input.vcf -o output.vcf --vcf --cache --offline - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 128
vep -i input.vcf -o output.vcf \ - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 151
vep -i input.vcf -o output.vcf --vcf \ - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 161
vep -i input.vcf -o output.vcf --vcf \ - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 193
conda install -c bioconda snpeff - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 200
snpEff ann GRCh38.105 input.vcf > output.vcf - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 206
snpEff ann -v -stats stats.html -csvStats stats.csv GRCh38.105 input.vcf > output.vcf - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 212
snpEff ann GRCh38.105 input.vcf | \ - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 229
SnpSift annotate dbsnp.vcf.gz input.vcf > annotated.vcf - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 246
SnpSift filter "(QUAL >= 30) & (DP >= 10)" input.vcf > filtered.vcf - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 256
annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/ - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 263
table_annovar.pl input.vcf humandb/ \
and 1 more places
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'variant-annotation' ] || [ -L ~/.agents/skills/'variant-annotation' ]; then echo 'A skill folder named variant-annotation already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-' "$d" && git -C "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation' ~/.agents/skills/'variant-annotation' && rm -rf "$d"; fi
Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'variant-annotation' ~/.claude/skills/'variant-annotation' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.
Badge for your README
The badge for mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills-/)
Score history
| Date | Version | Score |
|---|
| 2026-11-13 | fde6cd1 | 95 |
| 2026-11-07 | 839c35a | 100 |
Also found in
Identical copies of this skill exist at:
- BioTender-max/awesome-bio-agent-skills/skills/openclaw/variant-annotation
- lilinji/GeneTind-Life-Skills/skills/variant-interpretation-acmg/bioSkills/variant-annotation