Problem with alignment with pseudogenes

[swbarnes2]

You need to only use reads whose mates map in unique sequence in the region of the genome next to your real gene.

If the duplicated region is very large, this just might not work.

[alexanderxcy]

Hi All,

I am interested in discovering variants in a gene that has 4 pseudogenes on the same chromosome and 1 pseudogene on another chromosome. The sequence identity between the parent gene and the pseudogene ranges from 88% to 95%.

Currently we have paired-end reads and the aligned bam files for the chromosome that contains the gene. How do I avoid mapping the reads to pseudogenes?

Thanks!