Uveal Melanoma Cell line Analysis: SNVs, Indels and other variant calls. Circos plots of each genome.

Genomic DNA was extracted from cell lines using the Gentra Puregene Core Kit A (Qiagen) and library construction was performed using the NEBNext NEB Ultra II custom kit (New England Biolabs) according to the manufacturer’s instructions. Genomes were sequenced such that on average 79% of the genome of each cell line was covered by >30x coverage, with the remaining 20% covered by more than 10x sequence depth. Sequencing was performed by Illumina Hi Seq X Paired End Sequencing. SAMtools v1.10 was used to convert BAM files to FASTQ files. QC was performed using FastQC v0.11.8. Reads were aligned to GRCh38 using BWA mem v0.7.17. GATK v4.4.0.0 was used for germline short variant calling (SNVs, indels) with the HaplotypeCaller because these cell lines are clonal, not tumors. Germline variants were removed with bcftools using gnomAD data excluding all variants with an allele frequency >0.01. Identification of structural variants was performed using GRIDSS. Circos plots were generated in R v4.1.1 with StructuralVariantAnnotation v1.10.1, VariantAnnotation v1.40.0 and circlize v0.4.15 packages. Copy number calling was performed using CNVKit Version 0.9.8.