Method for detecting genetic variation in highly homologous sequences by independent alignment and pairing of sequence reads

A method for detecting genetic variation in a genome of a subject, the genome comprising highly homologous first and second regions of interest, the method comprising:

• (a) obtaining sequence reads by paired-end sequencing from multiple sites of interest in the first and second regions of interest, wherein the sequence reads comprise a first read and a second read obtained at each site of interest;
• (b) aligning sequence reads to a reference genome, wherein first reads and second reads are aligned to the reference genome separately and the aligner emits multiple possible alignments for each of the first and second reads;
• (c) identifying first reads and second reads that either:
• (i) align to the first region of interest;
• (ii) align to the second region of interest;
• (iii) sequentially align to the first and the second regions of interest;
• or
• (iv) align to the first and the second regions of interest in parallel;
• (d) pairing a first read and a second read from the reads identified in step (c), thereby generating a top paired alignment;
• and
• (e) detecting the genetic variation in the top paired alignment generated in step (d).