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variant-interpretation-acmg
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Check before installing.
By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c
Works with any agent that supports SKILL.md skills.
What this skill can do
Runs commands on your computer
The author does not mention this.
Found in 245 places.
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- skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 72
bcftools view -i 'INFO/CLNSIG~"Pathogenic" || INFO/CLNSIG~"Likely_pathogenic"' \ - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 103
bcftools view -i 'INFO/CLNREVSTAT~"multiple_submitters" || \ - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 116
git clone https://github.com/WGLab/InterVar.git - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 124
python Intervar.py \ - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 136
convert2annovar.pl -format vcf4 input.vcf > input.avinput - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 165
bcftools view -i 'INFO/gnomAD_AF<0.01 || INFO/gnomAD_AF="."' \ - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 179
bcftools view -i 'INFO/CADD_PHRED>20' input.vcf.gz -Oz -o cadd_filtered.vcf.gz - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 189
bcftools view -i 'INFO/REVEL>0.5' input.vcf.gz -Oz -o revel_filtered.vcf.gz - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 195
bcftools view -i '(INFO/CADD_PHRED>20 || INFO/REVEL>0.5) && \ - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 263
bcftools view -R gene_panel.bed input.vcf.gz -Oz -o panel_variants.vcf.gz - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 283
bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO/SYMBOL\t%INFO/Consequence\t\ - skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md, line 292
set -euo pipefail - skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md, line 34
bcftools consensus -f reference.fa input.vcf.gz > consensus.fa - skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md, line 40
bcftools consensus -f reference.fa -s sample1 input.vcf.gz > sample1.fa - skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md, line 46
bcftools consensus -f reference.fa -o consensus.fa input.vcf.gz - skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md, line 54
bcftools consensus -f reference.fa -H 1 input.vcf.gz > haplotype1.fa - skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md, line 60
bcftools consensus -f reference.fa -H 2 input.vcf.gz > haplotype2.fa
and 225 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, ftp.ncbi.nih.gov, gnomad-public-us-east-1.s3.amazonaws.com
The author does not mention this.
Found in 8 places.
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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-acmg' ] || [ -L ~/.agents/skills/'variant-interpretation-acmg' ]; then echo 'A skill folder named variant-interpretation-acmg already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/variant-interpretation-acmg' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/variant-interpretation-acmg' ~/.agents/skills/'variant-interpretation-acmg' && 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-acmg' ~/.claude/skills/'variant-interpretation-acmg' (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 lilinji/GeneTind-Life-Skills shows the score of its lowest-scoring skill.

[](https://zalavijaysinh.github.io/skilltrust/repos/lilinji/GeneTind-Life-Skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-11 | 908229c | 75 |