{"id":11048,"date":"2025-11-27T15:18:04","date_gmt":"2025-11-27T23:18:04","guid":{"rendered":"https:\/\/www.telemedical.com\/wordpress\/?page_id=11048"},"modified":"2026-05-26T22:21:31","modified_gmt":"2026-05-27T05:21:31","slug":"whole-genome-sequencing","status":"publish","type":"page","link":"https:\/\/www.telemedical.com\/wordpress\/whole-genome-sequencing\/","title":{"rendered":"Whole Genome Sequencing"},"content":{"rendered":"\n
<\/div>\n\n\n\n
\n
Provider<\/th>Typical WGS fee (test only)<\/th>Notes for research use<\/th>Notes<\/th><\/tr><\/thead>
Dante Labs<\/strong><\/a><\/td>30x WGS currently <\/td>Long\u2011standing global WGS seller; offers raw data and various health\/trait reports<\/td>$303 with discount
CODE TeleMedical<\/td><\/tr>

Nebula Genomics<\/a>

MyHeritage<\/a><\/td>		30x short\u2011read WGS<\/td>raw\u2011data export (FASTQ\/CRAM\/VCF) and positioned for privacy\u2011conscious users and downstream analysis.<\/td>$595
250 Reports
separate subscriptions for advanced reports.<\/td><\/tr>
Nucleus Genomics<\/a><\/td>30x clinical\u2011grade WGS with Z scores; includes 1 yr membership (~$39\/year) for ongoing risk\u2011model updates.<\/td>Clinical\u2011leaning WGS with polygenic scores and rare\u2011variant analysis; supports raw\u2011data export in standard formats for external tools.<\/td>$471 with discount code from drcarr@telemedical.com <\/td><\/tr>
Sequencing.com<\/a><\/td>Many WGS bundles<\/td>WGS or exome plus an \u201capp store<\/a>\u201d for interpretation and use with third\u2011party analytics.<\/td>$271\u2013$499 contact drcarr@telemedical.com for clinical study group based pricing.<\/td><\/tr>
<\/td><\/td><\/td><\/td><\/tr><\/tbody><\/table><\/figure>\n<\/div><\/div>\n\n\n\n

STR ( short tandem repeats) — microsatellites are long tandem repeats.<\/p>\n\n\n\n

    \n
  1. Long Read DNA <\/a>sequencing based determination from PacBio<\/a> , Oxford Nanopore Technol<\/a>ogies, or Illumina<\/a><\/li>\n\n\n\n
  2. For 30x short read WGS you typically do not impute<\/em> STRs; you directly genotype<\/strong> 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 <\/strong>\u2013 Haplotype\u2011based STR caller that takes aligned reads and a reference STR catalog; widely used for genome\u2011wide STR genotyping and has good accuracy on Illumina 30x.
    GangSTR<\/strong> \u2013 Uses paired\u2011end and insert size information to genotype both normal and expanded STRs from short\u2011read WGS.    <\/a>
    ExpansionHunter <\/strong>\u2013 Focused on pathogenic repeat expansions but also genotypes length variation at predefined loci; useful if you care mainly about known disease loci.
    TRTools \u2013 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.    <\/a>
    With 30x human WGS, the usual pipeline is: align with BWA\u2011MEM (or similar), call STRs genome\u2011wide 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\u2011chip or SNP\u2011only WGS data and want to impute STRs, the current standard approach is:
    STR reference panel + Beagle \u2013 The Gymrek lab built a 1000 Genomes SNP\u2013STR haplotype reference panel, and their SNPSTR imputation workflow uses Beagle (v4.1) to impute STR genotypes into SNP data.
    Example pipelines \u2013 The PD STR imputation pipeline (for Parkinson\u2019s) shows an end\u2011to\u2011end workflow: harmonize target GWAS SNP data to the SNP\u2013STR reference (using conform\u2011gt), then run Beagle for STR imputation, followed by QC and filtering of imputed STRs (e.g., DR2 > 0.3).
    So if your target<\/em> is SNP\u2011chip or sparse WGS and your reference<\/em> 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\u2011only samples.
    Tools summary
    <\/li>\n<\/ol>\n\n\n\n
    Step<\/th>Main tools<\/th>Notes<\/th><\/tr><\/thead>
    Call STRs from 30x WGS<\/td>HipSTR, GangSTR, ExpansionHunter<\/td>Short\u2011read callers; HipSTR is often default for genome\u2011wide work.diva-portal+2<\/td><\/tr>
    QC \/ downstream handling<\/td>TRTools<\/td>Harmonizes VCFs across callers, supports Beagle integration.trtools.readthedocs+2<\/td><\/tr>
    Build SNP+STR reference panel<\/td>HipSTR\/GangSTR + standard SNP callers + phasing<\/td>Approach used in 1000G and FinnGen STR reference panels.pmc.ncbi.nlm.nih+2<\/td><\/tr>
    Impute STRs into SNP\u2011only data<\/td>Beagle (often v4.1) with SNP\u2013STR panel, conform\u2011gt<\/td>Used by Gymrek SNPSTR pipeline and PD STR imputation pipeline.pmc.ncbi.nlm.nih+3<\/td><\/tr><\/tbody><\/table><\/figure>\n","protected":false},"excerpt":{"rendered":"

    Provider Typical WGS fee (test only) Notes for research use Notes Dante Labs 30x WGS currently Long\u2011standing global WGS seller; offers raw data and various health\/trait reports $303 with discountCODE TeleMedical Nebula Genomics MyHeritage 30x short\u2011read WGS raw\u2011data export (FASTQ\/CRAM\/VCF) and positioned for privacy\u2011conscious users and downstream analysis. $595250 Reportsseparate subscriptions for advanced reports. Nucleus […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-11048","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/pages\/11048","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/comments?post=11048"}],"version-history":[{"count":21,"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/pages\/11048\/revisions"}],"predecessor-version":[{"id":11532,"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/pages\/11048\/revisions\/11532"}],"wp:attachment":[{"href":"https:\/\/www.telemedical.com\/wordpress\/wp-json\/wp\/v2\/media?parent=11048"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}