genomic-coordinates

转换基因组区间并检测坐标系统不匹配问题

Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".

请帮我安装这个 Agent Skill：https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/genomic-coordinates

1. 先读取该目录下的 SKILL.md 和其他文件，检查是否有可疑内容（执行未知脚本、读取密钥、向外发送数据等），用中文告诉我它会做什么、需要哪些权限；
2. 等我确认后，再把整个目录安装到 ~/.claude/skills/genomic-coordinates/（如果你不是 Claude Code，安装到你自己约定的 skills 目录）；
3. 安装后告诉我怎么触发它。

git clone --depth 1 --filter=blob:none --sparse https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/genomic-coordinates-src
cd /tmp/genomic-coordinates-src && git sparse-checkout set "skills/genomic-coordinates"
mkdir -p ~/.claude/skills && cp -r "skills/genomic-coordinates" ~/.claude/skills/genomic-coordinates

Skill 可以让智能体执行脚本。安装第三方 Skill 前务必看一遍内容，详见「安全」一课。