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Multiple lanes of the same replicate were merged into a single FASTQ file before read trimming with SeqPurge [70] (version 0.1-886-gf72a054) and alignment on hg19 with HISAT2 [71] (v2.0.4). At each analysis step, FastQC [59] (v0.11.5) was used to check for quality and processing progress. Variants were called using Platypus [23] (v0.8.1). We note that duplicate reads were not removed prior to variant calling, as Platypus directly deduplicates BAM files during the calling process. BCFtools [57] (v1.9-207-g2299ab6) was used for variant annotation, filtering and selection. tabix (v1.6) and RTGtools [72] (v3.8.4) were used to manipulate the VCF files and compute basic statistics.

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