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Old 01-13-2015, 10:55 AM   #1
Location: Los Angeles, CA

Join Date: Jun 2012
Posts: 18
Default 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?
etwatson is offline   Reply With Quote
Old 09-23-2015, 12:42 PM   #2
Location: USA

Join Date: Apr 2010
Posts: 76

Did you figure out a solution? I'm running into the same problem 3 years later.
flobpf is offline   Reply With Quote

pca, plink, snp

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