Outputs from Fastq to Somatic Variants (Tumor Normal) (WGS)
The Fastq to Somatic Variants (Tumor Normal) (WGS) template workflow produces the following outputs:- Tumor Read Mapping A read mapping track for the tumor sample (
).
- Normal Read Mapping A read mapping track for the normal sample ().
- Somatic Variants The variant track (
) with the annotated variants.
- 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 Tumor Normal tool.
- Tumor Read Mapping Report A report () summarizing QC metrics, including coverage, for the tumor read mapping.
- Normal Read Mapping Report A report () summarizing QC metrics, including coverage, for the normal 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 tumor and normal Read Mappings 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).