comparison beagle4.xml @ 3:9e8de4ce2a3c draft

Added help notes to xml wrapper

2:e7e5432588ea

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3:9e8de4ce2a3c

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For a full guide, go to the Beagle4.0 documentation here: http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf

This wrapper allows for the selection of either a Genotype (gt) file, a Genotype Likelihood (gl) file or a Genotype (gt) plus Reference file as per the example usage here: http://faculty.washington.edu/browning/beagle/run.beagle.r1399.example

The only parameters currently exposed by this wrapper are impute-its and phase-its which both have default of 5. Please feel free to request more parameters to be made available by contacting bobbledavidson @ github.

Test data is available via the GitHub page: https://github.com/bobbledavidson/Beagle4Galaxy

Important note:
The creator of the Galaxy wrapper is not the same as the creator of the Beagle4.0 tool. All credit for the tool's abilities should be acknowledged using the following citation:

S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-97. doi:10.1086/521987

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