genomic-coordinates
Category: scientific-databases · License: MIT · Version: 1.1 · Includes scripts
Tags: genomic coordinates, liftover, variant normalization, genome assemblies, bioinformatics
When to use it
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”.Example requests
Ask your agent in plain language, for example:- “My peak caller output BED looks one base off when I load it next to my GTF annotations in IGV. What’s going on?”
- “I’m merging ClinVar (GRCh38 VCF) with my cohort’s VCF, but a bunch of known pathogenic indels in my samples (e.g. BRCA1 deletions in repeat regions) show up as novel. I’m doing a plain join on CHROM/POS/REF/ALT in pandas. bcftools says ‘REF does not match the reference’ for a few records too. How do I fix this?”
- “I have a transcript-level HGVS c.742C>T for a TP53 variant from a clinical report and need the genomic position so I can look it up in my aligned data. Which transcript, which strand, and how do I get to the genomic coordinate safely?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole scientific-databases category with /plugin install scientific-databases@research-agent-skills.