I am calling germline mutation using BWA and GATK pipeline.
RHD and RHCE gene share 97% homology.
The exon2 and exon8 of these genes are identical. So there is a high chance that the reads from these regions may map to each other and call false negative SNPs
How can I differentiate the true mapping read for each gene?
How to deal with identical exon region of Homologs gene for variant calling?
Are these things taken care of by BWA and GATK pipeline
Thank you in advance