GATK uses a series of algorithms to process raw sequencing data and identify genetic variants. The process typically includes the following steps:
Data Preprocessing: This involves cleaning and aligning the sequencing data to a reference genome. Variant Calling: This step identifies potential genetic variants such as SNVs (single nucleotide variants) and indels (insertions and deletions). Variant Filtering: This step filters out low-quality variants and retains only those that are likely to be true positives. Annotation: This involves adding biological context to the variants, such as their potential impact on gene function.
