Viral Amplicon Haplotype Calling

Question

[geneticatt]

I am working on a dataset produced from experimental evolution of a virus. Sequencing is Illumina paired end of a ~400bp amplicon. I would like to identify missense mutations evolved consistently in the experimental group which do not occur in the control group.

There are a number of programs designed for variant calling and haplotype reconstruction with similar tasks in mind. I see that GATK's HaplotypeCaller is a reliable tool, however there are several steps which are not relevant to an experiment where only the active region has been sequenced and each read pair spans the entire region. Freebayes looks promising for generating vcf files with which experimental and control groups can be compared.

I wonder if there are tools I am overlooking that are suitable for this type of analysis. If anyone has tool recommendations for this purpose, I would be grateful.

Answer 1

[geneticatt]

Update: It seems like a reasonable approach is to trim all amplicons to same size and positions relative to reference, translate these, then cluster the translated sequences. Cluster membership can be normalized by membership of same cluster in control sequences + 1.