Viral Genome SNP and Indel Detection

Question

[anjali.gopal91]

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, LoFreq, or Breseq, 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!

Answer 1

[Brian Bushnell]

If you are interested in detecting long indels, I highly recommend using BBMap for alignment, as it is the most accurate for detecting such mutations in my tests. Samtools mpileup and GATK are both capable of calling variants from sam files, and are widely used. I have also heard good things about FreeBayes, but note that it does not support the current SAM specification (which is already several years old), so you will need to add the sam=1.3 flag to BBMap's command line to generate old-style cigar strings that FreeBayes can process.