A small fraction of my reads are very short as shown on the attached figure. I'm assuming that this will have some negative impact on variant calling. I've removed reads that are too short after adaptor clipping, and thought this would be enough. However, there are clearly some that have slipped through.
Does anyone have any thoughts on this. I either have to add another read filtering step, or just leave it as it is in the knowledge that there aren't actually that many very short reads.
PS Note added in proof. From adding tags, I've just noticed that there's a read length filter tool - I guess I should use this.