Research Note: Evaluation of Resequencing Technologies Parameters for CNV Genotyping

Whole genome (re)sequencing provides new opportunities to discover Copy Number Variation (CNV) on the genome. Due to the continuous reduction in sequencing costs, it has become as the principal methodology to detect CNV in livestock. One parameter that increases the genotyping cost is the depth of the coverage during sequencing. The main aim of this note was to assess the variation on CNV identification with different depth coverage and readlength on genome sequencing. The results point out that sequences coming from short read-length require less depth coverage than those obtained with long read-length. In addition, small CNV require deeper coverage to be detected. These results can reduce the discovering and genotyping costs since sequencing technologies with short read-lengths are often less costly. Finally, a general formula was derived to optimize the sequencing costs.