genomic-coordinates
防止因组装或命名不匹配破坏下游分析，适合生物信息流水线。
处理基因组数据涉及敏感遗传信息，使用时需合规与脱敏。
在不同坐标约定和文件格式间转换、标准化并比较基因组区间与变体表示。
在不同文件格式、工具或参考基因组之间精确转换基因组区间和变体表示，比如 BED/GTF/VCF/SAM 等，并处理 0-based/1-based 差异、indel 左对齐与修剪、以及 assembly 或染色体命名不一致问题。当分析跨格式、跨工具或做 liftover、从基因组映射到转录本/CDS/蛋白位置时用最合适。特点是强制携带坐标的约定和 assembly 元数据，避免因格式错配毁掉下游分析。
▸ 展开 SKILL.md 英文原文
Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use 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".
帮我安装这个 skill：https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/main/skills/genomic-coordinates/SKILL.mdcurl -fsSL "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/main/skills/genomic-coordinates/SKILL.md"# Genomic Coordinates ## When to use Any time a coordinate crosses a boundary: between two file formats, between two tools, between two assemblies, or between the genome and a transcript. ## The rule **A coordinate is three facts, not one: the number, the convention it is written in, and the assembly it was measured against.** Carry all three or the number is not interpretable. Coordinate errors are the quietest class of bug in genomics. An off-by-one BED file parses, sorts, and intersects without complaint. A GRCh37 VCF joined against a GRCh38 annotation returns rows. A right-shifted indel simply fails to match its entry in ClinVar, and the result is a variant reported as novel. Nothin