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guoweilong / cgmaptools

toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR
https://cgmaptools.github.io
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CGmapTools-SNV calling for triploid organism #55

Open geethavenk opened 2 years ago

geethavenk commented 2 years ago

Hi, I am working with WGBS data from a triploid organism and would like to perform SNV calling using CGmapTools. The BayesWC strategy is based on the assumption of diploid genome. Would it be possible to use the tool for a triploid genome. How can the tool be adapted to a triploid genome.

Thank you. Geetha

guoweilong commented 2 years ago

Hi Geetha,

CGmapTools snp calling method is developed for diploid genome. Which species has triploid genome?

As I'm working on wheat study, which has an allo-hexaploid genome, and can be considered as diploid genome. If you are working on endosperm, I guess it could also be considered as diploid genome (at least, you can have a try).

Best, Weilong Guo

At 2022-01-18 19:15:58, "Geetha" @.***> wrote:

Hi, I am working with WGBS data from a triploid organism and would like to perform SNV calling using CGmapTools. The BayesWC strategy is based on the assumption of diploid genome. Would it be possible to use the tool for a triploid genome. How can the tool be adapted to a triploid genome.

Thank you. Geetha

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