--- title: Repeat expansion annotation from VCF file description: VarSome Clinical can annotate short tandem repeats (STR) VCF files produced by Oxford Nanopore, Illumina (Dragen), and PacBio. The VCFs uploaded to annotate STRs must meet the following requirements: --- [Skip to content](https://docs.varsome.com/en/repeat-expansion-annotation-from-vcf-file-1#main-content) English Show submenu for translations [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) [Customer portal](https://docs.varsome.com/support-requests?hsLang=en) [![varsome-new.png\]](https://docs.varsome.com/hs-fs/hubfs/varsome-new.png?height=40&name=varsome-new.png)](https://docs.varsome.com/en?hsLang=en) - Editions Show submenu for Editions - [VarSome.com](https://landing.varsome.com/varsome) - [VarSome Clinical](https://landing.varsome.com/varsome-clinical) - [VarSome Premium](https://landing.varsome.com/varsome-premium) - [VarSome API](https://landing.varsome.com/varsome-api) - [VarSome Insights](https://landing.varsome.com/varsome-insights) - About Show submenu for About - [The Company](https://saphetor.com/) - [Contact Us](https://landing.varsome.com/contact) - [Distributors](https://landing.varsome.com/distributors) - [Become a Partner](https://landing.varsome.com/become-varsome-partner) - [Community](https://varsome.com/community-contributions/) - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/) - Resources Show submenu for Resources - [Datasources](https://varsome.com/datasources/) - [Germline Classification](https://varsome.com/about/resources/germline-implementation/) - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) - [CNV Classification](https://varsome.com/about/resources/sv-implementation/) - [Help Center](https://docs.varsome.com/) - [Library](https://landing.varsome.com/whitepapers) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance) - Blog Show submenu for Blog - [Platform Updates](https://updates.varsome.com/en) - [Company News](https://news.varsome.com/en) - [VarSome Annotated](https://blog.varsome.com/annotated) Open main navigation Close main navigation - Editions Show submenu for Editions - [VarSome.com](https://landing.varsome.com/varsome) - [VarSome Clinical](https://landing.varsome.com/varsome-clinical) - [VarSome Premium](https://landing.varsome.com/varsome-premium) - [VarSome API](https://landing.varsome.com/varsome-api) - [VarSome Insights](https://landing.varsome.com/varsome-insights) - About Show submenu for About - [The Company](https://saphetor.com/) - [Contact Us](https://landing.varsome.com/contact) - [Distributors](https://landing.varsome.com/distributors) - [Become a Partner](https://landing.varsome.com/become-varsome-partner) - [Community](https://varsome.com/community-contributions/) - [Cite VarSome!](https://varsome.com/about/general/varsome-citations/) - Resources Show submenu for Resources - [Datasources](https://varsome.com/datasources/) - [Germline Classification](https://varsome.com/about/resources/germline-implementation/) - [Somatic Classification](https://varsome.com/about/resources/somatic-implementation/) - [CNV Classification](https://varsome.com/about/resources/sv-implementation/) - [Help Center](https://docs.varsome.com/) - [Library](https://landing.varsome.com/whitepapers) - [IVDR](https://landing.varsome.com/ivdr-whitepaper) - [Legal & Compliance](https://docs.varsome.com/en/legal-compliance) - Blog Show submenu for Blog - [Platform Updates](https://updates.varsome.com/en) - [Company News](https://news.varsome.com/en) - [VarSome Annotated](https://blog.varsome.com/annotated) - English Show submenu for translations - [Submit a Support Request](https://docs.varsome.com/en/kb-tickets/new) - [Customer portal](https://docs.varsome.com/support-requests) - [Contact us](https://docs.varsome.com/en/kb-tickets/new) [Contact us](https://docs.varsome.com/en/kb-tickets/new?hsLang=en) How can we help you? - There are no suggestions because the search field is empty. 1. [VarSome Help Center](https://docs.varsome.com/en?hsLang=en) 2. [Analysis of the results](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en) 3. [Analyses](https://docs.varsome.com/en/analysis-of-the-results?hsLang=en#analyses) # Repeat expansion annotation from VCF file VarSome Clinical can annotate short tandem repeats (STR) VCF files produced by Oxford Nanopore, Illumina (Dragen), and PacBio. The VCFs uploaded to annotate STRs must meet the following requirements: 1. Are compliant with the [VCF standard.](https://samtools.github.io/hts-specs/VCFv4.2.pdf) 2. The number of repeats is shown: 1. in the **ALT** field as \< STRn \> where *n* is the number of repeats for ONT, Dragen (ExpansionHunter), and 2. in the **MC** field for PacBio 3. The **INFO** field contains the repeat unit in the following format:  - - For ONT and Dragen (ExpansionHunter): ``` RU=GCC; SVTYPE=STR ``` - - For PacBio: ``` TRID=NOTCH2NLC; MOTIF=GGC; MC = 6,12 ``` #### **Useful information** - Minimum pathogenic repeat counts and maximum normal repeat counts are now retrieved from the [gnomAD](https://gnomad.broadinstitute.org/news/2025-03-known-disease-associated-tandem-repeat-pages/) STR dataset. - The tandem repeat genomic region (POS–END) and Repeat Unit (RU) fields (for ONT and DRAGEN), or the MOTIF field (for PacBio), are compared against the reference region and primary disease-associated repeat unit defined in the gnomAD STR dataset. Tandem repeats that fall within the reference region and share the same repeat unit as the locus of interest will display the corresponding gnomAD STR data. Additionally, gnomAD matching also includes adjacent repeats specified in the Locus Structure field of the gnomAD STR dataset and the ExpansionHunter variant catalog, when such structures are provided. \- For ONT data, the gnomAD RU is additionally checked against:   Display ‘**RU**’ if no match is found in the RU field.  \- For PacBio-derived VCFs, matching is performed against the primary disease-associated repeat unit only for this first phase. An example of a PacBio VCF header + its corresponding variant would be the following: ``` ##fileformat=VCFv4.2##FILTER=##INFO=##INFO=##INFO=##INFO=##FORMAT=##FORMAT=##FORMAT=##FORMAT=##FORMAT=##FORMAT=##FORMAT=##FORMAT=#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    HM16212-FXNchr6    170561906    .    GGCAGCAGCAGCAACAACAACAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA    GGCAGCAGCAGCAACAACAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA,GGCAGCAGCAGCAACAACAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCAACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCA    0    .    TRID=TBP;END=170562017;MOTIFS=GCA;STRUC=(GCA)n    GT:AL:ALLR:SD:MC:MS:AP:AM    1/2:102,111:94-121,93-123:141,132:34,37:0(0-102),0(0-111):0.950980,0.954955:1.00,0.79chr9    27573528    .    CGGCCCCGGCCCCGGCCCC    CGGCCCCGGCCCC,CGGCCCCGGCCCCGGCCCCGGCCCCGGCCCC    0    .    TRID=C9ORF72;END=27573546;MOTIFS=GGCCCC;STRUC=(GGCCCC)n    GT:AL:ALLR:SD:MC:MS:AP:AM    1/2:12,30:6-12,5-32:149,152:2,5:0(0-12),0(0-30):1.000000,1.000000:0.03,0.03 ``` --- The STR analysis from VCF is launched as a sub-analysis of the main analysis. You can launch a STR annotation by: - Adding an STR VCF file when defining your sample. 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