Usage instructions

1. Upload files

    VCF file:
    Upload a VCF file containing tumor specific somatic variant calls, preferably detected by the variant caller MuTect2. MuTect2 calls both point mutations and indels.
    If MuTect or MuTect2 has not been used for variant calling, genomic mutant allele frequencies will not be taken into account.
    The NGS analysis should preferably have been run by aligning and using the GRCh38 reference.
    If not, you can choose to upload a VCF from HG19 alignment, and check off the HG19 box; MuPeXI will then run a liftover of the VCF file to GRCh38.

    Expression file:
    Upload a tab-delimited file with expression values for each Ensembl transcript ID.
    Format: Ensembl Transcript ID <tab> Expression value (TPM) <tab> variance on call.
    This file can be obtained through RNAseq analysis with, for example, Kallisto.
    Transcript IDs must correspond to the GRCh38 v78 coordinates.

2. Select or enter the HLA alleles

    All HLA alleles present in the tumor should be provided.
    Example: HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03

3. Select peptide lengths

    Specify peptide length. Multiple lengths can be chosen.

4. Submit the job

Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.

At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.


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