Genomic Coordinates Agent Skill

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.