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varSEAK Open - FOR VCF FILE IMPORT
FROM OTHER SEQUENCING PIPELINES

varSEAK Open

varSEAK Open is intended for every genetic facility that does not use SEQUENCE PILOT (yet). The same functionality as in varSEAK Pilot is offered, based on the import of vcf-files from any sequencing analysis software.

  • HIGHLIGHTS

    • varSEAK Open Edition: for everyone not using SEQUENCE PILOT
    • Fast and reliable solution to manage, filter, interpret and classify genetic variants, based on a lab internal installation (varSEAK Open) which is connected to a global database and communication instance (varSEAK global server)
    • Easy import of VCF files with data from other sequencing pipelines into varSEAK Open
      • Import options include fields for Total Read Depth, Reference and Allele Read Depth, Variant Frequency and FILTER to keep information about variant quality
      • Variants can be filtered upon import using said fields and other filters such as regionsfiles, phenotypes and genelists
      • Import can be automated with programmatic access
    • Detailed lab internal classification of variants in varSEAK Open (includin HPO-compliant phenotypes, mode of inheritance, documents, weblinks, PubMed-IDs, medical reports…)

     

    • Connected to the varSEAK global database server to access bundled information:
      • Public databases (e.g. dbSNP, 1000 Genomes, ClinVar, ESP, ExAC, gnomAD, p53, UK10K, Mutation-Taster and SIFT)
      • ACMG compliant classifications from other varSEAK users
    • Highly flexible and adaptable functions to filter the detected variants (phenotype, genomic regions, genes/gene panels, splice site prediction, classifications, AF/MAF, etc.) with current data from the varSEAK global database
    • Automatic Splice Site Prediction for every imported variant with over 96% accuracy
    • Generation of individual variant reports for each patient
    • Internal communication tool to contact other users or labs that identified the same variant or variants in close genomic proximity
    • Optional submission of classified variants to the varSEAK global database (submitted data: the identified variant, the ACMG classification tier (1-5), the name of the lab)

     
  • varSEAK Open Edition: for everyone not using SEQUENCE PILOT
  • Fast and reliable solution to manage, filter, interpret and classify genetic variants, based on a lab internal installation (varSEAK Open) which is connected to a global database and communication instance (varSEAK global server)
  • Easy import of VCF files with data from other sequencing pipelines into varSEAK Open
    • Import options include fields for Total Read Depth, Reference and Allele Read Depth, Variant Frequency and FILTER to keep information about variant quality
    • Variants can be filtered upon import using said fields and other filters such as regionsfiles, phenotypes and genelists
    • Import can be automated with programmatic access
  • Detailed lab internal classification of variants in varSEAK Open (includin HPO-compliant phenotypes, mode of inheritance, documents, weblinks, PubMed-IDs, medical reports…)
  • Connected to the varSEAK global database server to access bundled information:
    • Public databases (e.g. dbSNP, 1000 Genomes, ClinVar, ESP, ExAC, gnomAD, p53, UK10K, Mutation-Taster and SIFT)
    • ACMG compliant classifications from other varSEAK users
  • Highly flexible and adaptable functions to filter the detected variants (phenotype, genomic regions, genes/gene panels, splice site prediction, classifications, AF/MAF, etc.) with current data from the varSEAK global database
  • Automatic Splice Site Prediction for every imported variant with over 96% accuracy
  • Generation of individual variant reports for each patient
  • Internal communication tool to contact other users or labs that identified the same variant or variants in close genomic proximity
  • Optional submission of classified variants to the varSEAK global database (submitted data: the identified variant, the ACMG classification tier (1-5), the name of the lab)