Hi
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 whjile 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?
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 whjile 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?