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bio-variant-calling-deepvariant

95 / 100 · Low risk

Fine to try. Some of what it can do is expected: a devops skill usually runs commands, installs tools and uses cloud credentials.

By lilinji/GeneTind-Life-Skills (GitHub) · devops · 17 stars · scanned at commit 908229c

Calls germline SNPs and indels with Google DeepVariant, which reframes variant calling as CNN image classification over multi-channel pileup tensors. Covers platform-specific model selection (WGS, WES, PACBIO, ONT_R104, HYBRID_PACBIO_ILLUMINA), one-shot run_deepvariant vs the three-stage make_examples/call_variants/postprocess_variants pipeline, GPU acceleration of call_variants, DeepTrio for family/trio and de-novo calling, and joint genotyping of gVCFs with GLnexus (not GenotypeGVCFs). Use wh…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-variant-calling-deepvariant' ] || [ -L ~/.agents/skills/'bio-variant-calling-deepvariant' ]; then echo 'A skill folder named bio-variant-calling-deepvariant 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 "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-variant-calling-deepvariant' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-variant-calling-deepvariant' ~/.agents/skills/'bio-variant-calling-deepvariant' && 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/'bio-variant-calling-deepvariant' ~/.claude/skills/'bio-variant-calling-deepvariant' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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