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Question: Extension to GoogleGenomics: getVariantCalls
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gravatar for Vincent J. Carey, Jr.
9 months ago by
United States
Vincent J. Carey, Jr.6.2k wrote:

We have introduced a function, getVariantCalls, into GoogleGenomics, that has

the same interface as getVariants, but returns a VRanges with genotype content for all samples.

The function has only been tested against the 1000 genomes variant datasets, and

at present does not acquire call-related information beyond the genotype, and does not

address phasing information.  The next version will address some of these limitations.

We would be interested to hear from users with related requirements.

install_github("vjcitn/GoogleGenomics", ref="variantcalls") # will get the branch with the new function

ADD COMMENTlink written 9 months ago by Vincent J. Carey, Jr.6.2k

Thank you Vince for your contribution.

This feature is now also included in the Bioconductor github repository, and will be in the next release.

ADD REPLYlink written 9 months ago by sidb0
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