Reads were first demultiplexed using the bcl2fastq conversion software (Illumina). Next, the reads were adapter- and quality-trimmed using BBDuk and optical duplicates removed using Clumpify. Both BBDuk and Clumpify are part of the BBTools and BBMap suite version 38.06 (https://sourceforge.net/projects/bbmap/). Reads were then aligned to the reference genome using BBMap and deletions called with the BBMap variant caller CallVariants. The number of reads mapping to a deletion was normalized relative to the total number of reads that aligned to the reference genome. This value was multiplied by 106 to obtain deletion event reads per million reads (RPM), as described previously2.

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