1. Upload file with mutations

• VCF file:
  Upload a VCF file with somatic mutations in the tumor, including point mutations and indels.
  Genomic positions must by default be in hg19/GRCh37 coordinates, unless otherwise specified
  See example.

• Genome version:
  Select the genomic coordinates used in your input files. Default is hg19/GRCh37.
  

2. Upload file with copy number aberrations (optional)

This part is optional. If this data is available, the full version of TumorTracer can be used, with more accurate predictions as a result.

• SEG file:
  Upload a segmentation file with somatic CNAs. The last column should contain a numeric representation of the copy number.
  Genomic positions must by default be in hg19/GRCh37 coordinates, unless otherwise specified.
  See example.

• Define cutoffs:
  Define cutoff values that will be applied to the numeric values in the segmentation file, and used to determine regions with deletions and amplifications. Note that the given cutoffs are exclusive.

3. 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.