Outputs from Fastq to Somatic Variants (WGS)
The Fastq to Somatic Variants (WGS) template workflow produces the following outputs:
- Read Mapping A read mapping track (
).
- Somatic Variants A variant track (
) with the annotated variants.
- Inversions An annotation track (
) providing the called inversions.
- Ignored Regions An annotation track () providing regions where it was not possible to
detect variants due to high complexity among the initial variants being tested.
- LightSpeed Report A report (
) summarizing details of each analysis step performed by the LightSpeed Fastq to Somatic Variants tool.
- Read Mapping Report A report () summarizing QC metrics, including coverage, for the read mapping.
- Sample Report A report () that contains compiled QC metrics from other reports and provides an overview of a given sample. The report contains a quality control section reflecting the summary items specified in the Create Sample Report wizard step.
- Amino Acid Track A track (
) providing a graphical representation of identified amino acid changes.
- Genome Browser View A track list (
) containing the Somatic Variants, the Ignored Regions, the Amino Acid Track, the Read Mapping as well as the Reference sequence and the Genes, mRNA and CDS tracks.
The Amino Acid Track is produced by Amino Acid Changes (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Amino_Acid_Changes.html).
The Read Mapping Report is produced by QC for Read Mapping (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Read_Mapping.html).