genomic-coordinates

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. Nothing raises an error; the answer is just wrong, and it is wrong in a direction that looks plausible.

So: convert with the table, not from memory, and verify against the reference whenever a reference is available.

The two conversions

1-based inclusive  ->  0-based half-open :  start - 1,  end
0-based half-open  ->  1-based inclusive :  start + 1,  end

The end coordinate never moves. If a conversion changed both numbers, it is wrong.

Which format is which

| 0-based, half-open | 1-based, inclusive | | --- | --- | | BED, bedGraph, bigWig, narrowPeak | GFF3, GTF, VCF | | BAM/CRAM (binary POS) | SAM (text POS) | | PSL, genePred, refFlat | WIG, Picard interval_list | | MAF (UCSC multiple alignment) | MAF (TCGA mutation annotation) | | PyRanges, pybedtools | GRanges/IRanges, samtools & UCSC & Ensembl region strings |

Both "MAF" formats exist, they mean different things, and they disagree. UCSC serves 0-based files through a 1-based browser box. references/format-conventions.md has the full table with per-format detail.

cd skills/genomic-coordinates/scripts

python3 convert_coords.py --list                          # the table
python3 convert_coords.py --from bed --to gff chr1 999 1000
python3 convert_coords.py --from ucsc --to bed "chr7:5,530,601-5,530,625"
python3 convert_coords.py --from granges --to pyranges --input regions.tsv

contig  input                 output           length  status  detail
chr7    chr7:5530601-5530625  5530600-5530625  25      ok

Zero-length BED features (chromStart == chromEnd, a legal insertion point) are reported as unrepresentable rather than converted to end = start - 1. Exit code is 1 when any interval is degenerate or invalid.

Variants are not intervals

A VCF POS for an indel is the anchor base — the base before the event, itself unchanged. And the same change can be written many ways: chr1:7:CAC:C, chr1:3:CAC:C and chr1:2:GCA:G are one deletion. Joining, deduplicating, or looking up variants before normalising loses real matches silently, and it loses them preferentially in repeats, where indels concentrate.

Normalise — trim to parsimony, then left-align against the reference — before any comparison:

python3 normalize_variant.py --fasta ref.fa chr1 7 CAC C
python3 normalize_variant.py --fasta ref.fa --split --input cohort.vcf
python3 normalize_variant.py --fasta ref.fa --compare chr1:7:CAC:C chr1:2:GCA:G

input         normalized    type      pos_shift  ref_check  changed
chr1:7:CAC:C  chr1:2:GCA:G  deletion  5          ok         yes

Every record's REF is checked against the FASTA first. A MISMATCH means the variants and the reference are different assemblies — stop and run check_contigs.py rather than adjusting coordinates. Multi-allelic records must be split with --split before normalising, never after.

HGVS shifts indels the opposite way, 3'-most along the transcript. For a minus-strand gene that is the opposite genomic direction from VCF's left-alignment. Details and the full procedure: references/variant-representation.md.

Check the assembly before trusting a join

python3 check_contigs.py --identify unknown.fa.fai
python3 check_contigs.py variants.vcf annotation.gtf --genome GRCh38.fa.fai

file          kind    contigs  naming        assembly  detail
ref.fa.fai    sizes   25       plain         GRCh37    24/24 primary chromosome lengths match;
                                                       chrM is 16569 bp, i.e. GRCh37/38 (rCRS MT)

The script reads .fai, .chrom.sizes, VCF headers, SAM headers, FASTA, BED, and GTF/GFF, identifies the assembly from primary-chromosome lengths, and reports every reason a join between two files would go wrong: naming mismatch, length conflict, coordinates past a contig end, contigs present in one file only. Exit code 1 on any incompatibility.

GRCh37 and hg19 differ only in the mitochondrion — 16,569 bp (rCRS) versus 16,571 bp. Nuclear coordinates are identical, so a mixed pipeline runs fine and only the mtDNA results are wrong. check_contigs.py reports which one it found. Builds, naming schemes, ALT contigs, and liftover pitfalls: references/reference-builds.md.

Audit a file against its own format

python3 audit_intervals.py peaks.bed
python3 audit_intervals.py gencode.gtf --genome hg38.chrom.sizes
python3 audit_intervals.py cohort.vcf --genome GRCh38.fa.fai

Looks for the evidence that a coordinate mistake leaves behind:

| Finding | What it proves | | --- | --- | | start_below_one in GFF/GTF | 0-based data in a 1-based file; everything is one base left | | many_zero_length in BED | 1-based single-base features written into a 0-based file | | past_contig_end | wrong assembly, or an off-by-one at the contig edge | | mixed_contig_naming | any join will silently match one subset | | first_block_offset | BED12 blockStarts written as absolute coordinates | | not_parsimonious | untrimmed alleles; normalise before joining | | bad_alt_allele | Ensembl/VEP - notation in a VCF, which has no anchor base |

Exit code 1 on any fatal finding, so it works as a CI gate on a data directory.

Transcript, CDS, and protein positions

c.742 and chr17:7,674,220 are both "position", and neither converts to the other by arithmetic. Transcript coordinates count spliced bases in transcription order — decreasing genomic coordinate on the minus strand — and c.1 is the A of the initiator ATG, not the start of the transcript.

The rules that get mis-remembered: there is no c.0; 5' UTR positions are negative and 3' UTR positions take a *; GFF phase is the bases to remove to reach the next codon, not start % 3; and a c. description is meaningless without a versioned transcript accession, because the same variant numbers differently in each transcript. references/transcript-coordinates.md has the conversion procedure and the boundary cases.

Do the conversion with a tool that holds the transcript model — VEP, bcftools csq, Mutalyzer, the hgvs package — not by hand.

Reporting results

State the assembly next to the coordinates, every time. chr7:5,530,601-5,530,625 is not a location; chr7:5,530,601-5,530,625 (GRCh38) is. Say which convention a coordinate column is in, in the column header or the file's documentation. When a conversion produced a result, say which direction it went.

References

• references/format-conventions.md — every format's convention, with per-format detail, BED12 block rules, region-string syntax, and tool behaviour.
• references/variant-representation.md — VCF allele conventions, the normalisation algorithm, equivalence checking, multi-allelic splitting, and how HGVS disagrees with VCF.
• references/reference-builds.md — build signatures, GRCh37 vs hg19, ALT contigs, naming schemes, and liftover failure modes.
• references/transcript-coordinates.md — genomic ↔ transcript ↔ CDS ↔ protein, HGVS numbering, phase, and transcript choice.