Based on the documentation about the necessity of a mask file and other related questions, it seems that the mask file should specify regions where reads were not mapped and variants were not called.
I attempted to generate a BED file of unmapped regions from a BAM file using bedtools complement. However, I am unsure if this is the correct approach.
bedtools complement -i smc_Pinc-p1_s.bam -g pinc_chr.genome.txt > p1_mask.bed
Thank you for your help!