Question: How to run PLINK from a personal computer
0
gravatar for ccolmenares
18 months ago by
ccolmenares0 wrote:

Hi! This is my situation. I recieved a file in impute2 version and I need to do a mendelian randomization analysis. My plan was:

1. Convert the file to a plink format
2. Import those files in R
3. Do the GWAS analysis
4. Select de SNP's associated with a specific trait
5. Import data to Stata, build the genetic score and do the MR analysis

This make sense to you?

I downloaded Plink 1.07 and it runs in my personal computer but when it starts this comes up:

Web-based version check ( --noweb to skip )
Recent cached web-check found...Problem connecting to web

Writing this text to log file [ plink.log ]
Analysis started: Wed Feb 14 17:36:17 2018

Options in effect:

Before frequency and genotyping pruning, there are 0 SNPs
0 founders and 0 non-founders found
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 0 SNPs

ERROR: Stopping as there are no SNPs left for analysis

And I cant run any command because it says: it is not recognized as an internal or external command

What can I do?

plink • 1.2k views
ADD COMMENTlink modified 18 months ago • written 18 months ago by ccolmenares0
1

Before frequency and genotyping pruning, there are 0 SNPs

It just complains there are no SNPs in your input file. Have you checked that file?

ADD REPLYlink written 18 months ago by WouterDeCoster40k

First, try PLINK 1.9 : https://www.cog-genomics.org/plink/1.9/

ADD REPLYlink written 18 months ago by Maxime Lamontagne2.1k

Hey Maxime, I already tried and it's the same situation Thanks

ADD REPLYlink written 18 months ago by ccolmenares0
1

Could you post your command.

ADD REPLYlink written 18 months ago by Maxime Lamontagne2.1k

cant run any command because it says: it is not recognized as an internal or external command

This usually means that the executable that you're trying to run is not in your PATH. Ensure you've added the directory in which the executable it to your PATH.

ADD REPLYlink written 18 months ago by RamRS23k

Hi Ram, Already adjusted the path and I been able to run the program. I received files like this PA_gwas_chr_1_python_filtered.impute2.gz and I want to generate .bed. and .fam files but I really do not know how... I apreciatte any advice, I'm new to those softwares. Thanks!

ADD REPLYlink modified 18 months ago by RamRS23k • written 18 months ago by ccolmenares0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

ADD REPLYlink written 18 months ago by genomax70k

Check WouterDeCoster's comment: C: How to run PLINK from a personal computer

ADD REPLYlink written 18 months ago by RamRS23k
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