SNP calling in Identical exons of two different genes

Question

[Sudhir Jadhao]

Hello Everyone,

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?

OR

Are these things taken care of by BWA and GATK pipeline

Thank you in advance

[Nicolas Rosewick]

GATK should normally use only primary alignment for SNP calling (or am I wrong ?)

[Sudhir Jadhao]

Yes, but how does it handle the identical exon SNP calling?