Paula Ruiz-Rodriguez1
and Mireia Coscolla1
1. I2SysBio, University of Valencia-CSIC, FISABIO Joint Research Unit Infection and Public Health, Valencia, Spain
Pairwise genetic distance matrices from allele-frequency data. Fstic reads single-sample VCFs or frequency tables and computes eight standard estimators (FST, GST, Jost's D, Reynolds, Nei, Cavalli-Sforza chord, Rogers, Bray-Curtis) in parallel, writing an N x N matrix.
It is built for data where a sample is not a single genotype but a frequency spectrum: mixed infections, deep-sequenced isolates, pooled populations.
pathogenomics-lab.github.io/fstic
| Tutorial | Four samples from raw VCFs to a tree, finding a mixed infection on the way. Ten minutes, no downloads. |
| Installation | Bioconda, or building from source. |
| Input formats | What Fstic reads from a VCF or a table, and what it skips. |
| Choosing an estimator | All eight formulas, their ranges, and when disagreement between them means something. |
| Filtering | Setting thresholds for consensus, within-host and deep amplicon work. |
| Command-line reference | Every flag, with defaults and exit codes. |
| How it works | The model the estimators rest on, and what stops a run rather than warning. |
conda install -c bioconda fsticOr build it, which needs a Rust toolchain:
git clone https://github.com/PathoGenOmics-Lab/fstic.git
cd fstic && cargo build --releaseOne VCF per sample, named after the sample:
fstic --vcf TB-*.vcf --output distances.csvsample,TB-001,TB-002,TB-003
TB-001,0.0000000000,1.0000000000,7.0000000000
TB-002,1.0000000000,0.0000000000,8.0000000000
TB-003,7.0000000000,8.0000000000,0.0000000000Those are cumulative totals, not values in [0, 1]. Adding --normalize divides
by the locus count and gives 0.125, 0.875 and 1.0 instead.
Pick an estimator, normalise per locus, and tighten the filters:
fstic --vcf-list samples.txt \
--output chord.tsv \
--formula chord \
--min-depth 50 \
--min-af 0.01 \
--pass-onlyNote
--formula fst sums the per-locus Nei GST across sites, so it
grows with the locus count and is not bounded by 1. Use --normalize for the
mean, or --formula gst for a bounded ratio. The
estimator guide
explains the difference.
Ruiz-Rodriguez, P. and Coscolla, M. Fstic: allele-frequency-based genetic distance calculator. Zenodo. doi:10.5281/zenodo.16813662
Please cite the original paper for whichever estimator you used as well; they are listed on the citation page.
Bug reports with a reproducer are the most useful thing you can send. See contributing for building, testing and adding an estimator.
cargo test && cargo clippy --all-targets
