VCF-format: VCF objects in Siccuracy
In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

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:

Imputation_accuracy: imputation_accuracy
Writing SNP data: write.snps.vcfR

No functions have been implemented for VCF files. The functions above all assume the files have been read in with read.vcfR.

Direct conversion from VCF formatted files to AlphaImpute may be done by first using PLINK to recode to 'A' format, and then use convert_plinkA. 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:

convert_plinkA('temp_file.raw', 'alphaimpute_genotypes.txt')

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 <sme@iysik.com>, August 2017

stefanedwards/Siccuracy documentation built on May 30, 2019, 10:44 a.m.