genomic-coordinates
Skill1 starsChanged 51 days agoNo licenceView on GitHub
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".
1 other project uses a version of this, 1 of them edited.
Adopted by
Most recently taken up by
- patoangolano/bio-stackedited, first seen Oct 15, 2026
Other versions1 project uses a version of this.
Word for word · 0
None found.
Edited · 1
- patoangolano/bio-stack★ 063% same
Wrote their own version · 0
None found.
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3 rules. About 0 are common, 0 are distinctive, and 3 are very specific to this project.
≈0
Common · estimate
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3
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