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-   -   plink2 to EIGENSOFT .geno conversion (http://seqanswers.com/forums/showthread.php?t=49518)

etwatson 01-13-2015 11:55 AM

plink2 to EIGENSOFT .geno conversion
 
Hi all,

I have used plink2 for my project, and now have a database of .ped, .map, .bim, .fam, etc... files. I am interested in trying a new program to perform a PCA analysis for population structure among my samples that requires a database in the EIGENSOFT format (.geno, with genotypes coded as 0, 1, or 2 reference alleles).

My samples are non-model species, so I have had to use the --allow-extra-chr option in plink2 to get around the fact that there are thousands of chromosomes (scaffolds).

Using the convertf program packaged with EIGENSOFT did not work, since the number of chromosomes > 23 (come on!).

Does anyone know of any other conversion software/approach that may work for me?

flobpf 09-23-2015 01:42 PM

Did you figure out a solution? I'm running into the same problem 3 years later.


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