I am using hg38 as a reference for mapping in bwa-0.7.17. I have already created the 5 BWA index files for my reference fasta file. Since it's advisable to also take into consideration the alternate contigs (hg38DH.fa.alt); I wanted to ask if: 1. How do we include the file containing decoy sequences (hg38DH-extra.fa) in the alignment process.
In case the decoy file is needed, does it need to be in the same folder as the other index files.
If the bwa index files for the ALT contigs need to be present.