HG38 human reference is the collection of reference from all 22 chromosomes,x,y chromosomes, and some others. I was targeting to split the reference file into 22 chromosomes fasta files. I am following this link https://crashcourse.housegordon.org/split-fasta-files.html to split the fasta files.More specifically I want to split the fasta file into all possible (placed,unlocalized and unplaced) sequence and the merge placed and localized sequences. However, I am unsure where to put the HLA part of the reference. Should I put it in Chromosome 6? Also, should I dump the unknown chromosomes as I am specifically interested in chromosomes 1-22?
Any suggestion on splitting the fasta file into 22 chromosomes would be nice.