strand information for SNPs from VCF file (convert into IMPUTE format)

Question

[miaowzai]

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?

Thanks!

[sricham]

Hi Miaowzai .. were you able to get an answer for this?

Answer 1

[miaowzai]

I found a tool to do this: https://github.com/biocore-ntnu/snpflip