WGS of methotrexate-treated Dark agouti female rat tumor 51
FASTQ reads were aligned to the rat reference (mRatBN7.2) using Illumina DRAGEN BioIT Platform v4.0.3 (v07.021.645.4.0.3). Data from multiple flowcells were aggregated via @RG tags; alignment uses seed/exact matches refined by SmithWaterman. Tumour libraries were processed separately, and PCR/optical duplicates were marked within DRAGEN. Somatic variants were then called with DRAGEN v4.0.3 using its standard workflow: activeregion detection, local haplotype assembly, readlikelihood estimation, and ploidyagnostic genotyping to capture lowfrequency alleles.