Entering edit mode
7.3 years ago
nrcolumbia
•
0
Hi,
I am attempting to create PC's using Eigensoft but keep getting this error:
fatalx:
(getpedgenos) "filename".ped bad geno I
Aborted
Could anyone help me understand what could be going wrong here? I am using pruned .map files. Here is the script:
genotypename: trial.ped
snpname: trial.map
indivname: trial.ped
outputformat: EIGENSTRAT
genotypeoutname: trial.eigenstratgeno
snpoutname: trial.snp
indivoutname: trial.ind
Thank you!
Kinda hard to make a guess without seeing your data, but based on the error message I suspect that one of your genotypes is encoded as "I" in your .ped file. Does that make sense?
Thanks for the reply. Do you mean that for a particular sample, instead of alleles there may just be an "I" represented in the .ped file? Do you know how I may go about testing for this? Thanks again!
I would suggest a simple grep
grep -w "I"
but I don't know your operating system.Yes - I found the "I"s. Thanks for your help!