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SNP calling in Identical exons of two different genes

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

genome alignment snp homolog identical exon
• 1,492 views • link
written by Sudhir Jadhao Sudhir Jadhao

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

• 1 views • link
written by Nicolas Rosewick Nicolas Rosewick

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

• 0 views • link
written by Sudhir Jadhao Sudhir Jadhao

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