Phasing SNPs in pedigrees (mini linkage)

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Hi,
I have about 5000 variants on one chromosome that I would like to phase in a few families. I have the data from NGS in a tab delimited format. Can this be done with Galaxy tools?
thanks

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Hi @kingab,
Beagle seems to the most suitable tool for performing such analysis, but currently is it not available in Galaxy; If you consider it appropriate (or have any other suggestion) it can be included.

Regards

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Hi @gallardoalba,
thanks a lot for your reply. I would find this application very useful, however I am not sure if you need to reach a ‘critical mass’ of interest before introducing new tools to Galaxy… thanks for considering!
Regards,
Kinga

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I’ll work on it, doesn’t seem a very complex tool to implement; I will try to make it available for next week.

Regards

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Wow, that’s amazing thanks @gallardoalba !

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Hello @gallardoalba, I was wondering if you ware able to implement the Beagle to galaxy… thank you,
K

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Hi @kingab,
a PR has been opened in order to include this tool: Pull Request #3760.

Regards

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thanks so much!

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