FASTQ files were demultiplexed using cutadapt [21] based upon barcodes identifying DNA source and replicate number, and the barcodes and adapter sequences were trimmed from each read. The UMI was then trimmed and stored in the read name using umi_tools [22]. Using bwa-mem [23], remaining reads were mapped to the reference sequences defined by the reference and alternative sequence for each SNP of interest. Finally, umi_tools was used to count the number of UMI-unique reads for each sequence.
