Response to Comment on 'DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification'

Following the Comment of Stewart et al ., we repeated our analysis on sequencing runs from The Cancer Genome Atlas (TCGA) using their suggested parameters. We found signs of oxidative damage in all sequence contexts and irrespective of the sequencing date, reaffirming that DNA damage affects mutation-calling pipelines in their ability to accurately identify somatic variations.