Conditional analysis on dosage file -what program to use?

Question

[datanerd]

HI all,

i have recived some files that I fail to understand the header as the dosage info is ok with 3 probabilities for each sample.

This was used for the association analysis in plink list skip0=0 skip1=0 format=3 case-control-freqs

PLINK v1.90b3.43 64-bit (13 Nov 2016) Options in effect: --allow-no-sex --covar file.covar --covar-number 4 --dosage file.gprobs.list list skip0=0 skip1=0 format=3 case-control-freqs --fam file.fam --out result.assoc --pheno file.pheno

However, I cannot do conditional analysis on this. So was hoping to convert them to ped to do conditional. Can someone help me how to convert and/or understand the file format to make ped file.

Thanks so much!!!

Answer 1

[pfs]

I would install plink2 and then run the command - plink2 --gen '..gen', --missing-code 'what missing values are encoded as in your .sample file' --sample '..sample' --oxford-single-chr 'chr_num' . This should get you started.