I have .gprobs, .metrics and .sample output file from IMPUTE2 and am trying to run association test using PLINK. I have uploaded first 5 lines of chromosome 12 here:
- .gprobs: https://dl.dropboxusercontent.com/u/6723585/IMPUTE2/Chr12_head_5.gprobs
- .metrics: https://dl.dropboxusercontent.com/u/6723585/IMPUTE2/Chr12_head_5.metrics
- .sample: https://dl.dropboxusercontent.com/u/6723585/IMPUTE2/Chr12_head_5.sample
I have tried to run
--dosage analysis using the .gprobs file and .sample to do the association test on a chromosome level.
But I am getting several warnings for:
- "Duplicate individual found"
- ERROR: Badly aligned columns for: SNP A1 A2
I have also tried to convert .gprobs and .sample to native ped and fam using gtools and tried the association test using PLINK but the output files also did not worked with
--assoc command. I am wondering if there any file conversion required before taking IMPUTE2 output to PLINK or Do you recommend any other tool for association testing using IMPUTE2 output ?
PS. I have tried to ask this question(s) to IMPUTE2 mailing list, but they haven't approved me even after 24 hours after confirming my email.