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Variant_Interpretation
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Check before installing.
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 36 places.
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- Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 85
bcftools view -i 'INFO/CLNSIG~"Pathogenic" || INFO/CLNSIG~"Likely_pathogenic"' \ - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 116
bcftools view -i 'INFO/CLNREVSTAT~"multiple_submitters" || \ - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 129
git clone https://github.com/WGLab/InterVar.git - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 137
python Intervar.py \ - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 149
convert2annovar.pl -format vcf4 input.vcf > input.avinput - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 178
bcftools view -i 'INFO/gnomAD_AF<0.01 || INFO/gnomAD_AF="."' \ - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 192
bcftools view -i 'INFO/CADD_PHRED>20' input.vcf.gz -Oz -o cadd_filtered.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 202
bcftools view -i 'INFO/REVEL>0.5' input.vcf.gz -Oz -o revel_filtered.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 208
bcftools view -i '(INFO/CADD_PHRED>20 || INFO/REVEL>0.5) && \ - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 276
bcftools view -R gene_panel.bed input.vcf.gz -Oz -o panel_variants.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 296
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/SYMBOL\t%INFO/Consequence\t\ - Skills/Genomics/Variant_Interpretation/bioSkills/clinical-interpretation/SKILL.md, line 305
set -euo pipefail - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 41
bcftools annotate -a dbsnp.vcf.gz -c ID input.vcf.gz -Oz -o annotated.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 56
bcftools annotate -a dbsnp.vcf.gz -c ID input.vcf.gz -Oz -o with_rsids.vcf.gz - Skills/Genomics/Variant_Interpretation/bioSkills/variant-annotation/SKILL.md, line 62
bcftools annotate -a database.vcf.gz -c ID,INFO/AF,INFO/CAF input.vcf.gz -Oz -o annotated.vcf.gz - 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
and 16 more places
Downloads and installs other software
The author does not mention this.
Found in 4 places.
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Sends data to these websites: ftp.ncbi.nlm.nih.gov
The author does not mention this.
Found in 2 places.
Safer alternatives
Low-risk skills in the same category (other) that look related. Check that one does what you need.
Install
Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.
if [ -e ~/.agents/skills/'variant-interpretation' ] || [ -L ~/.agents/skills/'variant-interpretation' ]; then echo 'A skill folder named variant-interpretation 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 "$d" checkout --quiet 'fde6cd1025d8a9300ad783b3d6696fa708a5cdb0' -- 'Skills/Genomics/Variant_Interpretation' && mkdir -p ~/.agents/skills && cp -R "$d"/'Skills/Genomics/Variant_Interpretation' ~/.agents/skills/'variant-interpretation' && 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-interpretation' ~/.claude/skills/'variant-interpretation' (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 | 75 |
| 2026-11-07 | 839c35a | 75 |