Hi Joseph, thanks for the feedback. We do not want to use BreakDancer as it requires paired-end data to call deletions (correct me if I'm wrong). We have our own in-house code for doing this and it works relatively well, but we want something independent of the sequencing mode. This is why I'm exploring split-reads alignment. DELLY might be worth looking into (wasn't aware of the tool, so thanks for pointing it out!), but it comes with additional dependencies and we want to distribute our code without forcing end-users to spend days installing all required software packages. The beauty of using samtools, I hoped, would be that deletion calling would be integrated with SNP/indel calling this way, and everything would end up in a single output file.
Thanks again and best wishes, Wolfgang On 03.06.2014 20:24, Joseph Fass wrote: > Hi Wolfgang, > > AFAIK, samtools can only call short variants (SNPs / indels), despite > the fact that you'll see evidence in the raw mpileup format. I think > you'd need to use something like BreakDancer, DELLY, or even SGA's > graph-diff tool (I'm experimenting with this for longer insertions, but > don't have any conclusions yet. > > Others probably have better suggestions; this isn't an area I know very > well ... > > ~Joe > ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
