Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
Fig 1
Bamgineer conceptual overview.
Haploype-specific CNVs simulated using re-paired reads. Red and blue colors represent read-pairs corresponding to different haplotypes. Purple color represents new reads corresponding to the red haplotype. A. Original BAM file used as the input. B. Allele-specific loss, reads matching a target haplotype are removed C. Allele-specific single copy number gain (CN = 3). D. Allele-specific 2-copy gain (CN = 4). In C and D, new read pairs are constructed from existing reads and reads are modified at SNP loci to match the desired haplotype.