SEQanswers

Go Back   SEQanswers > Applications Forums > Genomic Resequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
National Geographic and Family Tree DNA Announce Geno 2.0 KerryOdair Personalized Genomics 17 08-12-2013 08:18 AM
PubMed: VarioWatch: providing large-scale and comprehensive annotations on human geno Newsbot! Literature Watch 0 12-13-2012 11:40 PM
PubMed: Snat: a SNP annotation tool for bovine by integrating various sources of geno Newsbot! Literature Watch 0 10-11-2011 02:00 AM

Reply
 
Thread Tools
Old 01-13-2015, 10:55 AM   #1
etwatson
Member
 
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
flobpf
Member
 
Location: USA

Join Date: Apr 2010
Posts: 76
Default

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

Tags
pca, plink, snp

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:13 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO