I notice that when short reads are mapped to highly polymorphic region (e.g. HLA genes), the reads that are not similar to the reference genome will be much less likely to be mapped.
What is the best way to deal with this? For the case of HLA, I think I can add a bunch of HLA sequences to the reference genome file to let mappers map these reads there.
Are there better way to handle this? Thanks
What is the best way to deal with this? For the case of HLA, I think I can add a bunch of HLA sequences to the reference genome file to let mappers map these reads there.
Are there better way to handle this? Thanks