When LongTR or HipSTR is used for STR genotyping, the allele numbers derived from their output sometimes differ from those in reference databases, CE-based profiles, or other forensic tools. A D2S441 allele that should be reported as 11.3 may appear as 11.8 when its length in base pairs is converted to repeats by dividing by the motif length, for example in a spreadsheet such as Excel formatted to one decimal. No error is raised. The software has performed correctly. The discrepancy is a consequence of two incompatible naming conventions applied to the same underlying sequence, and it can be resolved with a straightforward arithmetic conversion.

What is the GB field?

LongTR and HipSTR do not store allele numbers directly in the VCF. Instead, they record the number of base pairs by which each allele differs from the reference sequence at that locus. This value is stored in a field called GB, short for GenotypingBases.

A real vcf output line looks like this:

4|1:-1|8:1.00:0.50:16:0:0:0|0:0|0:28.03:-2|1;-1|5;8|8;9|1;12|1:-1|6;8|10

In this line GB is the second field, right after GT: -1|8. The FORMAT column gives the order of the fields, so read the position of GB there rather than assuming it.

The pipe symbol separates the two alleles:

-1 means allele 1 is 1 base pair shorter than the reference
+8 means allele 2 is 8 base pairs longer than the reference

Every allele number in the final genotype is derived from these two values together with the reference information in the BED file used during genotyping.

The GB field in a LongTR / HipSTR VCF output line

For D2S441 in hg38, the relevant BED file values are:

ref_repeats = 12 (the reference carries 12 complete repeat units; its CE designation is also 12)
period = 4 bp (the motif is TCTA, four bases long)
Reference size = 12 × 4 = 48 bp

Walking through the calculation

Following allele 1 (GB = -1) step by step:

Step 1. Total base pairs of this allele:

Reference: 12 repeats × 4 bp = 48 bp GB = -1 Allele 1 total = 48 - 1 = 47 bp

Step 2. This is where a division-based conversion and ISFG diverge.

Dividing total base pairs by the motif length and rounding to one decimal place gives:

47 ÷ 4 = 11.75 → rounded: 11.8

The LongTR and HipSTR VCF does not contain this decimal: GB is an integer (here -1). The 11.8 comes from a conversion step like this one, for example a spreadsheet such as Excel showing 11.75 with one decimal, not from the VCF.

ISFG convention asks a different question: how many complete repeat units fit into 47 bp, and how many bases remain?

47 bp = 11 complete TCTA repeats (44 bp) + 3 extra bases ISFG notation: 11.3

Both values describe the same physical sequence of 47 base pairs. The difference lies entirely in how the partial component is expressed: the division gives a rounded decimal fraction of a repeat unit, while ISFG reports the count of extra bases directly.

From 47 bp to allele 11.3: dividing by the motif length versus ISFG counting

Allele 2 requires no correction: GB = +8 → 48 + 8 = 56 bp → 56 ÷ 4 = 14.0 → no partial repeat → ISFG: 14.

Why this matters

Forensic population databases, including CODIS reference data, ESS frequency tables, and published population studies, use ISFG notation exclusively. An allele designated 11.8 does not appear in any of these resources. Submitting an allele converted this way without correcting it will return no database match and produce no error message. The discrepancy is silent and, if undetected, will affect likelihood ratio calculations and cross-platform profile comparisons.

The same issue arises when validating long-read results against CE-based profiles from the same individual or against known reference samples.

The conversion rule

If you meet decimals produced by dividing by the motif length, this table maps them back to extra bases for tetranucleotide loci. It only translates the decimal. The allele number itself has to start from the CE designation of the reference allele for that locus, genome build and window (for D2S441 in hg38, CE 12). At other loci, flanking indels or historical length conventions can make the arithmetic differ, so this is not a general algorithm.

Decimal (÷ 4, rounded)	Extra bases	ISFG suffix
.3	1	.1
.5	2	.2
.8	3	.3

The pattern holds because the division computes extra bases ÷ period and rounds. For a tetranucleotide locus, 3 extra bases give 3 ÷ 4 = 0.75, which rounds to .8. ISFG writes the same situation as .3, counting the extra bases directly.

Confirmed affected loci when using the standard HipSTR hg38 BED file:

.8 → ISFG .3: D1S1656, D2S441, D6S1043, D12S391, TH01

.5 → ISFG .2: D18S51, D19S433, D21S11, FGA

Summary

LongTR and HipSTR encode allele information as a base-pair difference from the reference sequence, stored in the GB field of the VCF. Applying this difference to the reference size gives the allele length in base pairs. Dividing that length by the motif length gives a decimal that, once rounded, is not an ISFG designation. ISFG notation instead counts the complete repeat units and the extra bases that remain, starting from the CE designation of the reference allele for the locus. For tetranucleotide loci, a rounded .8 corresponds to 3 extra bases, which ISFG writes as .3. The conversion must be applied before any database query, likelihood ratio calculation or cross-platform profile comparison.

References

Frontanilla Recalde T, Ayala Jacquet JM, Mendes Junior CT et al. (2026). HipSTR-UI: A cross-platform graphical interface for accessible STR genotyping from next-generation sequencing data. Forensic Science International: Genetics, 84, 103456. https://doi.org/10.1016/j.fsigen.2026.103456
Valle-Silva G, Frontanilla T, Ayala J, Donadi EA et al. (2022). Analysis and comparison of the STR genotypes called with HipSTR, STRait Razor and toaSTR by using next generation sequencing data in a Brazilian population sample. Forensic Science International: Genetics, 58, 102676. https://doi.org/10.1016/j.fsigen.2022.102676
Gettings KB, Bodner M, Borsuk LA, King JL, Ballard D, Parson W et al. (2024). Recommendations of the DNA Commission of the International Society for Forensic Genetics (ISFG) on short tandem repeat sequence nomenclature. Forensic Science International: Genetics, 68, 102946. https://doi.org/10.1016/j.fsigen.2023.102946
Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y. (2017). Genome-wide profiling of heritable and de novo STR variations. Nature Methods, 14(6), 590–592. https://doi.org/10.1038/nmeth.4267
Ziaei Jam H, Zook JM, Javadzadeh S et al. (2024). LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads. Genome Biology, 25, 176. https://doi.org/10.1186/s13059-024-03319-2