lumpy fails to call tandem duplications that are shorter than the sequencing read length

[ruomu-helix]

Hi lumpy devs,

We have been using lumpy to call SVs on our Exome sequencing data ( 2 x 150bp). It generally has pretty good sensitivity. However we notice that it consistently fails to call duplications that are shorter than our read length. For a short dup, eg ~80bp, all the reads supporting the dup will be soft-clipped and there are no discordant read pairs like there are for longer dups. Even though the soft-clipped reads clearly point to a dup, lumpy doesn't call it. Curiously, lumpy seems to call short deletions with no problem, which also only have signals from soft-clipped reads. We surmise that lumpy's algorithm must require both types of signal to call a dup, but not a del. In contrast, we tried Manta on the same data and it calls the short dup with no problem. We are wondering if there are parameters we can tweak to make lumpy call the dups using only signals from soft-clipped reads. Thanks!

Ruomu