What problem does it solve? Coordinate errors are the quietest class of bug in genomics: an off-by-one BED file parses and intersects without complaint, a GRCh37 VCF joined against GRCh38 annotation returns rows, and a right-shifted indel silently fails to match its ClinVar entry. This Skill converts intervals between coordinate conventions correctly, normalizes variant representations, and audits files for convention violations before they corrupt an analysis. ## Core Features & Use Cases - Coordinate Conversion: Convert intervals between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, and region strings, reconciling 0-based half-open with 1-based inclusive conventions. - Variant Normalization: Trim and left-align indels against a reference FASTA, split multi-allelic records, and check whether two variant records describe the same change. - Assembly and Convention Auditing: Identify GRCh37 vs hg19 vs GRCh38 vs T2T from contig lengths, detect chr-prefix mismatches, and audit BED/GTF/VCF files for convention violations as a CI gate. - Use Case: Before joining a cohort VCF against a GENCODE annotation, run the contig check to confirm both files use the same assembly and naming scheme, then normalize the variants so indel lookups against ClinVar actually match. ## Quick Start Ask the AI to convert chr7:5,530,601-5,530,625 from UCSC browser coordinates to BED format and audit your peaks.bed file for coordinate convention violations.
