How to tackle homeologous region which calling SNP for Allotetraploid genome

Question

[Kritika]

Hello

I recently got SNP analysis of allotetraploid genome(AADD genome type) My steps are

Fastqc

Trimming

next is mapping onto reference genome

My concern is with homoelogous region how should i tackle this while mapping?

Is there quality filtering parameter which can tackle homoelogous region and give true SNPs and Indels

Also what are concern should i put while doing QC and trimming?

[Titus]

Hi, I work with human panel in which we got homoelogous region/genes. I checked and with bwa default parameters we have alignment for both region. So if your reads are longer than your homoelogous regions you will detect your SNP, but if you got 100% similarity region it will be impossible to distinguish regions.