Output from the Identify Somatic Variants from Tumor Normal Pair (WGS) workflow

Seven different outputs are generated:

  1. Read Mapping Tumor (Image read_track_16_n_p) The mapped sequencing reads for the tumor sample. The reads are shown in different colors depending on their orientation, whether they are single reads or paired reads, and whether they map unambiguously (see Mapped reads coloring).
  2. Read Mapping Normal (Image read_track_16_n_p) The mapped sequencing reads for the normal sample. The reads are shown in different colors depending on their orientation, whether they are single reads or paired reads, and whether they map unambiguously.
  3. Mapping Report Tumor (Image proteinreport_16_n_p) The report consists of a number of tables and graphs that in different ways provide information about the mapped reads from the tumor sample.
  4. Mapping Report Normal (Image proteinreport_16_n_p) The report consists of a number of tables and graphs that in different ways provide information about the mapped reads from the normal sample.
  5. Amino Acids Changes Track that shows the consequences of the variants at the amino acid level in the context of the original amino acid sequence. A variant introducing a stop mutation is illustrated with a red amino acid.
  6. Annotated Somatic Variants (Image variant_track_16_n_p) A variant track holding the identified and annotated somatic variants. The variants can be shown in track format or in table format. When holding the mouse over the detected variants in the Genome Browser view a tooltip appears with information about the individual variants. You will have to zoom in on the variants to be able to see the detailed tooltip.
  7. Genome Browser View Tumor Normal Comparison (Image trackset_16_n_p) A collection of tracks presented together. Shows the annotated variants track together with the human reference sequence, genes, transcripts, coding regions, the mapped reads for both normal and tumor, the annotated somatic variants, information from the ClinVar database, and finally a track showing the conservation score (see figure 15.25).

Image identify_somatic_variants_genomebrowserview_wgs
Figure 15.25: The Genome Browser View presents all the different data tracks together and makes it easy to compare different tracks.