[Samtools-help] Tools to remove read given region?

[Wibowo A. <bo...@bo...>]

Dear samtools list,

I was wondering if the Picard suite has a tool to wipe reads from a
BAM file given a list of targeted regions?

My use case is to remove all reads mapping to known ribosomal RNA
regions. While there are tools to do simple reads removal out there
(e.g. bedtools), what I am looking for is to have as if the reads in
the given region were never mapped in the first place. For example, if
read01 maps to a ribosomal RNA gene and another gene, the tools would
remove read01 from both the rRNA gene and the other gene (taking into
account pairing structure, MAPQ values, and others of course).

I have been browsing around the Picard website to find such a tool,
and the most close I can find is the FilterSamReads tool. So just to
double-check in case I may be reinventing something, I am wondering if
someone has developed something like this :).

Best regards,
Bow