To allow fluid interaction with the Variant Call Format, some functions accepts the objects from the vcfR package.
The following functions have been implemented with method dispatching for vcfR objects:
No functions have been implemented for VCF files.
The functions above all assume the files have been read in with
Direct conversion from VCF formatted files to AlphaImpute may be done by
first using PLINK to recode to 'A' format, and then use
For the first step, PLINK may be called as:
plink --vcf <vcf-filename> --recode A --allow-extra-chr --out temp_file
and then to convert to AlphaImpute format:
Take care of sample IDs when using PLINK, as IDs containing an underscore ('_') are split into family ID and sample ID (famID and sampID, respectively).
Stefan McKinnon Edwards <[email protected]>, August 2017
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