Questions about how to use this aligner

[jazybio]

1) For the alignment of the human whole exome sequence FASTA data to the human GRCh38p14 reference genome, and using the Isaac aligner V4, do you recommend:

• unmasked genome reference ?
• masked genome reference ?
• reference with hs38d1 decoy sequence included ?

2) Please define how the human reference genome sequences are masked for best use with Isaac aligner V4 and human exome FASTA alignment ?

• is it a soft mask ?
• is it a hard mask ?

3) For the alignment of the human whole genome sequence FASTA data to the human GRCh38p14 reference genome, and using the Isaac aligner V4, do you recommend:

• unmasked genome reference ?
• masked genome reference ?
• reference with hs38d1 decoy sequence included ?

4) To mark and remove PCR duplicates from the BAM file generated from either human exome or human whole genome FASTA, what parameters are set with Isaac aligner V4:
Option 1:
--keep-duplicates 1 or --keep-duplicates 0

OR
Option 2:
--mark-duplicates 1 or --mark-duplicates 0