Mask regions with high coverage in pacbio bam file
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
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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).