bedtools intersect -abam (bam) -b rRNA.bed -v should be able to handle this.
On Sep 30, 2014, at 9:18 PM, Nils Homer wrote:
> Hey Bow,
>
> unfortunately there is no single tool that would perform your task. While
> you could try to chain various tools together, the difficulty in this process
> is to make sure that the mate information for paired reads is updated
> correctly. If you want some tips on developing such a tool for your own use,
> I would be happy to discuss this off-list,
>
> N
>
> On Mon, Sep 29, 2014 at 6:56 AM, Wibowo Arindrarto <b...@bow.web.id> wrote:
> 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
>
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