Question: Best tool for variant calling in polyploids
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gravatar for giannkas1
11 months ago by
giannkas10
giannkas10 wrote:

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!

snp assembly genome • 282 views
ADD COMMENTlink modified 11 months ago by harish300 • written 11 months ago by giannkas10
0
gravatar for harish
11 months ago by
harish300
harish300 wrote:

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

ADD COMMENTlink written 11 months ago by harish300

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

ADD REPLYlink written 11 months ago by giannkas10
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