is there a tool or script which can remove reads from my bam files which contain soft clipped bases? It would be nice if I could also define to just remove reads that have at least n soft clipped bases, or the fraction of soft clipped bases is more than x.
@Pierre to rescue: Remove Soft Clipped Bases
How to remove reads with hard/soft clipping along with its mate?
This seems to remove only the soft clipped bases. But I'd like to get rid of the whole reads.
There are two links in the post. Did you look at the second?
Oh, sorry haven't seen your edit.
But in your first link I also found a link to bamutils. A combination of removeclipping and filter seems to fit my needs. It's only a pity that bamutils seems not to support streaming.
Thanks for showing me the right direction.
It's probably a bit late as you already have a BAM but if you really don't want any read clipped, your probably best off forcing your aligner to align entire reads (e.g. bowtie2 end-to-end).