TEvarSim: A genome simulator for transposable element (TE) variants
Fig 3
Validation of simulated genomes.
(A) Comparison of TE variants recorded in the VCF file (left) versus those extracted from CIGAR strings in the BAM file after minimap2 alignment (right). A discrepancy in one TE deletion is highlighted with an arrow. (B) When the sequence of the TE deletion in question was mapped to both GRCh38-Chr21 and the simulated genome, it aligned fully to GRCh38-Chr21 but not to the expected location in the simulated genome, indicating that the deletion was successfully introduced. This sequence had four multi-mapped positions on the reference and three on the simulated genome, likely contributing to the minimap2 mapping artifact.