Mask regions with high coverage in pacbio bam file

Question

[junnna]

Hi,
I would like to filter out regions with >50x coverage from a pacbio hifi bamfile such that the resulting filtered bam file has zero coverage in those regions.
I tried variantbam https://github.com/walaj/VariantBam, like so: variant $bam -m 100 -o mini.bam -b but this gives me an error:
removeElem: elem of value -1 is below min bin 0,0,0
Any ideas would be greatly appreciated!
Thanks in advance

[GenoMax]

Is your BAM file sorted? Are you actually substituting the name of your BAM file in place of $bam?

Additional options:

https://ngsutils.org/modules/bamutils/extract/ (use an inverted BED file to select regions you want to keep).