Reads mapping Sample Clauses

Reads mapping. In this step, we perform read mapping using the personalized diploid reference genome instead of the universal NCBI reference genome. Although we use map- ping software BWA v0.5.9 [36] with default parameters in this study, our pipeline scheme can accommodate any read mapping software The raw output of the mapping step cannot be used directly because reads are mapped against a diploid reference genome that contains many “mini chromosomes”. We take another step to process the mapping result such that reads mapped to “mini chromosomes” are correctly interpreted as mapped to the corresponding genomic location with the alternative allele present at the middle SNP. This step contains two parts: first, the correct genomic mapping locations are recovered; second, none- zero quality scores are assigned according to some confidence values. Figure 2.2 demonstrates the whole process of our pipeline.