PLINK format to EIGENSTRAT format

Question

[bsmith030465]

Hi,

Is there a tool (apart from 'convertf') that can change PLINK output files (e.g. .ped) to EIGENSTRAT format? In this case, the PED file would be converted to a file with one line per SNP and one column per sample, and the range of values would be 0,1,2,9

thanks!

[chrchang523]

Er, is there some sort of problem you're having with convertf? It's definitely the standard tool for this job.

[bsmith030465]

1. The linux version of the package was downloaded from: http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html
2. The software seems to work for samples in the hundreds, but not in the thousands. The output file gets truncated at 2 GB - perhaps a 32-bit issue (README file)?

Answer 1

[chrchang523]

It looks like fcGENE is capable of this.

Answer 2

[Joey]

Already answered here.

A: Conversion tools for GWAS