Best tool for variant calling in polyploids
1
0
Entering edit mode
3.1 years ago
giannkas1 • 0

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 • 820 views
ADD COMMENT
0
Entering edit mode
3.1 years ago
harish ▴ 430

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1276 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6