Question: PLINK format to EIGENSTRAT format
2
gravatar for bsmith030465
4.6 years ago by
bsmith030465140
United States
bsmith030465140 wrote:

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!

eigenstrat plink • 5.4k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 4.6 years ago by bsmith030465140
1

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

ADD REPLYlink written 4.6 years ago by chrchang5234.9k

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)?

 

ADD REPLYlink written 4.6 years ago by bsmith030465140
0
gravatar for chrchang523
4.6 years ago by
chrchang5234.9k
United States
chrchang5234.9k wrote:

It looks like fcGENE is capable of this: http://sourceforge.net/projects/fcgene/

ADD COMMENTlink written 4.6 years ago by chrchang5234.9k
0
gravatar for Joey
4.6 years ago by
Joey410
Seattle
Joey410 wrote:

Already answered here.

A: Conversion tools for GWAS

ADD COMMENTlink written 4.6 years ago by Joey410
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