Hi all,
I'm trying to call snps and indels for HIV, and I'm wondering if there are suggestions for good mutation detection software for viruses. I expect to have fairly large indels (20-30bp in a 9kb genome), as well as the regular snps, across multiple samples that are pooled together in one run.
I'm probably going to try SNVer (http://snver.sourceforge.net/), LoFreq (http://sourceforge.net/p/lofreq/wiki/Home/), or Breseq (http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing), but I'm also wondering if there are any other software packages that would specifically be good at detecting indels.
Are there any recommendations for software?
Thanks!