I'm trying to do imputation by IMPUTE2 with a VCF file.
To generate the input files, I used plink: ./plink --vcf file.vcf --recode oxford --chr 1 --out output
Then I got four files: output.gen, output.sample, output.nosex and output.log
The basic IMPUTE2 requires inputs including output.gen, and also a strand file indicating the strand information of each SNPs in the output.gen file.
I'm not very familiar with the chip data and I'm not sure if I understood correctly, but I remember all SNPs in VCF files should be on the + strand. Does that mean all SNPs in the .gen file converted from vcf are strand +?
How can I get this strand file for my data?