GATK offers several key features that are particularly valuable in cancer genomics:
Accurate Variant Calling: GATK's variant callers, such as HaplotypeCaller and Mutect2, are highly accurate in identifying both single nucleotide polymorphisms (SNPs) and insertions/deletions (indels). Data Preprocessing: Tools like BaseRecalibrator and IndelRealigner improve the quality of sequencing data, making downstream analyses more reliable. Scalability: GATK can handle large datasets, making it suitable for large-scale cancer genomics projects like The Cancer Genome Atlas (TCGA).
