| Provider | Typical WGS fee (test only) | Notes for research use | Notes |
|---|---|---|---|
| Dante Labs | 30x WGS currently | Long‑standing global WGS seller; offers raw data and various health/trait reports | $303 with discount CODE TeleMedical |
Nebula Genomics MyHeritage | 30x short‑read WGS | raw‑data export (FASTQ/CRAM/VCF) and positioned for privacy‑conscious users and downstream analysis. | $595 250 Reports separate subscriptions for advanced reports. |
| Nucleus Genomics | 30x clinical‑grade WGS with Z scores; includes 1 yr membership (~$39/year) for ongoing risk‑model updates. | Clinical‑leaning WGS with polygenic scores and rare‑variant analysis; supports raw‑data export in standard formats for external tools. | $471 with discount code from drcarr@telemedical.com |
| Sequencing.com | Many WGS bundles | WGS or exome plus an “app store” for interpretation and use with third‑party analytics. | $271–$499 contact drcarr@telemedical.com for clinical study group based pricing. |
STR ( short tandem repeats) — microsatellites are long tandem repeats.
- Long Read DNA sequencing based determination from PacBio , Oxford Nanopore Technologies, or Illumina
- For 30x short read WGS you typically do not impute STRs; you directly genotype them from the BAM/CRAM and, if needed, impute only residual missing calls or into SNP-only datasets using an STR reference panel.
Direct STR genotyping tools (30x WGS)
These are what you would usually run on your 30x WGS alignments:
HipSTR – Haplotype‑based STR caller that takes aligned reads and a reference STR catalog; widely used for genome‑wide STR genotyping and has good accuracy on Illumina 30x.
GangSTR – Uses paired‑end and insert size information to genotype both normal and expanded STRs from short‑read WGS.
ExpansionHunter – Focused on pathogenic repeat expansions but also genotypes length variation at predefined loci; useful if you care mainly about known disease loci.
TRTools – Not a caller itself, but a toolkit that ingests VCFs from HipSTR, GangSTR, ExpansionHunter, etc., and supports downstream QC, filtering, and also integrates with Beagle for imputation of TR genotypes.
With 30x human WGS, the usual pipeline is: align with BWA‑MEM (or similar), call STRs genome‑wide with HipSTR or GangSTR using a reference STR catalog, then use TRTools for harmonization, filtering (call quality, depth, stutter metrics), and format conversion.
STR imputation into SNP data (when needed)
If you instead have SNP‑chip or SNP‑only WGS data and want to impute STRs, the current standard approach is:
STR reference panel + Beagle – The Gymrek lab built a 1000 Genomes SNP–STR haplotype reference panel, and their SNPSTR imputation workflow uses Beagle (v4.1) to impute STR genotypes into SNP data.
Example pipelines – The PD STR imputation pipeline (for Parkinson’s) shows an end‑to‑end workflow: harmonize target GWAS SNP data to the SNP–STR reference (using conform‑gt), then run Beagle for STR imputation, followed by QC and filtering of imputed STRs (e.g., DR2 > 0.3).
So if your target is SNP‑chip or sparse WGS and your reference is 30x WGS with STR calls, you:
call STRs on the 30x WGS using HipSTR/GangSTR,
build an SNP+STR reference panel,
use Beagle (or equivalent) to impute STRs into the SNP‑only samples.
Tools summary
| Step | Main tools | Notes |
|---|---|---|
| Call STRs from 30x WGS | HipSTR, GangSTR, ExpansionHunter | Short‑read callers; HipSTR is often default for genome‑wide work.diva-portal+2 |
| QC / downstream handling | TRTools | Harmonizes VCFs across callers, supports Beagle integration.trtools.readthedocs+2 |
| Build SNP+STR reference panel | HipSTR/GangSTR + standard SNP callers + phasing | Approach used in 1000G and FinnGen STR reference panels.pmc.ncbi.nlm.nih+2 |
| Impute STRs into SNP‑only data | Beagle (often v4.1) with SNP–STR panel, conform‑gt | Used by Gymrek SNPSTR pipeline and PD STR imputation pipeline.pmc.ncbi.nlm.nih+3 |