Calling Snp From Sample Containing Quasispecies

Question

[SJL]

Hi all,

I have sequenced a virus genome using Illumina. As viruses are evolving rapidly, I suspect that there is more than one genotype in my "pure" sample - one dominant and many satellite genotypes. When I sequenced a batch of viruses I have a crazy coverage of more than 10,000X for some of them. So, I am wondering if it is possible to look at the alignment of the reads to the assemblies to find possible Hot Spots that accumulate mutations.

Which program/algorithm should I use to address this question ?

Any comments/suggestions are welcome.

Thank you

Answer 1

[Andreas]

Hi SJL,

in this paper we've developed a method called LoFreq (see also the corresponding Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data) that can detect very low frequency variants (wet-lab verified down to 0.5%) and makes no assumptions on ploidy. Other programs to mention in this context are SNVer (with corresponding ploidy and filtering settings) and Breseq. In the paper we also analyzed hotspots and coldspots in Dengue virus samples (see Methods for a short description). An alternative way of analysis is to assemble the haplotypes (with for example Shorah) but the crazy coverage is usually a problem for haplotype assemblers and also the usual variant callers, whereas LoFreq is optimized for such cases.

Andreas

[Andreas]

Also check out http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245950/ (hot off the press)