Stop-gains and frameshifts are collectively prevalent in humans and could be responsible for some of the inter-individual variability in phenotypes. Current computational approaches evaluating loss-of-function in genes carrying these variants rely on gene-level characteristics such as evolutionary conservation and functional redundancy across the genome. NUTvar uses sequence-based features (such as loss of functional domains, isoform-specific truncation and non-sense mediated decay) in a Bayesian classification scheme to rank variants according to their potential for loss-of-function. NUTvar complements existing gene-based pathogenicity scores.

The NUTvar analysis pipeline and data used is described in the original article:
Analysis of stop-gain and frameshift variants in human innate immunity genes Rausell A, Mohammadi P, McLaren PJ, Bartha I, Xenarios I, Fellay J, Telenti A (2014)

The pipeline's software can be downloaded from here.

Contact:

  • antonio.rausell at isb-sib.ch
  • amalio.telenti at chuv.ch

Usage instructions

Please fill in your affiliation and contact information in the below form and upload a VCF file from your machine. Computational time might be long for large input files. You will be notified by email when process is finished.
Input file:
VCF format (example)
Output file:
Output file: Compressed tar.gz file containing two tab-delimited text files with NUTvar assessment of stop-gain and frameshift variants that were found in the input file. A description of the outputfile format and content is described here.
Disclaimer
Please do not upload VCF files with individual genotype information, those fields are not needed for this analysis. Do not upload privacy sensitive data. We record your email address and affiliation to keep track of the usage of this service and to notify you once the analysis is finished. IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR SERVICE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE OR SERVICE.