Best tool for variant calling in polyploids

Question

[giannkas1]

To whom read this question, I hope this message finds you well.

I am trying to build a genetic map for sugarcane and as I understand, one of the first steps is to call for variants. I have a sequenced (WGS data) bi-parental population of 95 sugarcane individuals (including both parents). I already aligned them (Bowtie2 and Picard to generate sorted bams) to their reference genome (a specific cultivar) with high percentage of alignment but now I need to call for variants. I am using NGSEP (https://github.com/NGSEP/NGSEPcore) (using MultisampleVariantsDetector instruction) to call for SNVs, small and large indels, STRs, inversions, and CNVs. However, it is taking a lot of time (I think, it has an inconvenient because it doesn't have the option to parallel) and I would like to have an alternative, e.g. I launched just 20 individuals last Thursday, September 19th and it has not ended yet.

Any help is really appreciated, thank you!

Answer 1

[harish]

Why not try Freebayes? It has an option to split up the variant calls to parallelize as well as account for polyploids.

[giannkas1]

This one: https://github.com/ekg/freebayes I haven't tried it but I will.