plink running issue

[emilyjia2000]

Hello,

when I tried to run plink with option --file, it always gave me an error message, for example,
plink --file mydata.vcf

I expected mydata.ped and mydata.map were generated, instead of that, it gave me an error message as below.

@----------------------------------------------------------@
| PLINK! | v1.07 | 10/Aug/2009 |
|----------------------------------------------------------|
| (C) 2009 Shaun Purcell, GNU General Public License, v2 |
|----------------------------------------------------------|
| For documentation, citation & bug-report instructions: |
| http://pngu.mgh.harvard.edu/purcell/plink/ |
@----------------------------------------------------------@

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: Sun Jan 8 21:48:40 2012

Options in effect:
--file mydata.vcf


ERROR: No file [ mydata.vcf.ped ] exists.

Anyone knows what's wrong with my command?

Thanks a lot.

[dpryan]

From a cursory glance at the documentation, I'm going to guess that mydata.vcf.ped and mydata.vcf.map don't exist. You're telling plink to read them as input with the --file argument.

[emilyjia2000]

Thanks for the reply. Do you know how to use plink to generate .ped and .map files? I presumed that this command could help to generate those.

[dpryan]

vcftools, though I don't know if it generates the proper pedigree associations, since I'm not sure how pedigree information is specificed in a vcf file (not something I've ever needed to look into).

[emilyjia2000]

Thanks dpryan, i used vcftools to generate PED file, which brought a trouble to me when I used it for the linkage analysis. When I checked back and found out the some of genotypes from PED doesn't match to SNP calls (original results). so I would like to use plink.

[dpryan]

It's unclear what you mean when you say some of the values in the generated ped file didn't match the vcf file. An actual error message or example line would be helpful there. From what I can see, plink has no capability to convert vcf to ped/map files, so you'd be best either writing your own converter or using vcftools, if it's screwing something up then you should submit a bug report.

[emilyjia2000]

Hi Dprayn,

I don't exactly know if it counts. When I tried to used ped file generated by vcftools from vcf file to do linkage analysis, there are a lot of Mendelian errors were generated based on ped file, I checked a couple of genotypes flagged with error compared to the vcf (original SNP call), and found out that it should be correct in the vcf file. So I guess only likely reason is converted ped file might not be completely correctly converted from vcf.

[dpryan]

Sounds like you should submit a bug report to the people who make vcftools. See if you can make a small .vcf file that can be used to recreate the error and then send a query to their email list.

[emilyjia2000]

Thanks for the suggestion, I will do it.