Reference of Whole exome sequecing analysis

Question

[Shahzad]

Dear all

I am new for WES analysis and want to ask which human reference genome should i download for Whole Exome analysis. Please share a direct link to the genome assembly and also the gtf/gff3 file if it should be used. It is very confusing with so many variants of human genome i.e masked, unmasked, alt, rm, toplevel etc.

Best Regards Shahzad

Answer 1

[lakhujanivijay]

I prefer downloading from iGenomes

This link should have pre-indexed genome files that you require