variant calling using masked reference genome

Question

[reza]

hi

I want to start a variant calling process using reference genome. Since most reference genomes in NCBI are masked (Some parts of the genome are marked with small letters), do I need to convert lowercase to uppercase before starting the process?

Will the manipulation or non-manipulation of the reference genome affect the final results?

Thanks

[Pierre Lindenbaum]

duplicate Behaviour Of Aligners For Occurence Of Lowercase And Upper Case Bases In A Fasta File