# Analysis Methods

The software processes sequencing data to perform quality control, detect variants, determine tumor mutational burden (TMB), microsatellite instability (MSI) status, and genomic instability score (GIS), and report results. The following sections describe the analysis methods used in DRAGEN TruSight Oncology 500 Analysis Software.

DRAGEN TruSight Oncology 500 Analysis Software uses the following workflows to analyze sequencing data.

* FASTQ Generation
* DNA Analysis
  * DNA Alignment and Error Correction
  * Small Variant Calling and Filtering
  * Copy Number Variant (CNV) Calling
  * BRCA Large Rearrangements
  * Annotation
  * Tumor Mutational Burden (TMB) Scoring
  * Microsatellite Instability (MSI) Status
  * Genomic Instability Score (GIS)
    * Tumor purity (beta)
    * Ploidy (beta)
  * Absolute Copy Number (beta)
  * Gene-level Losss of Heterozygosity (LOH) (beta)
  * Contamination Detection
* RNA Analysis
  * Downsampling
  * Read Trimming
  * Alignment
  * Fusion Calling and Filtering
  * Splice Variant Calling
  * Fusion Merging
  * Annotation
* Quality Control
  * Run QC
  * DNA Sample QC
  * RNA Sample QC


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