We discovered one of our hybrid capture probes designed in hg19 have two regions in hg38, and they are 98% homologous with each other. Thus when we use BWA to align, both areas get the same alignment score and a subsequent mapping score of 0, which is ignored by all downstream processes. Is there any way to get BWA to just assign the mapping score to both regions so that they are not ignored downstream, we filter with a bed file of regions later so the alt region would then be filtered out and only variants on the region of interest would be considered.
We have tried BWA flags -5, -q , -j
To no beneficial effect Thanks for any help you can provide! .