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Generating .ped and .map files from .dose.vcf.gz files

Hi Everyone,

I am now trying to generate .ped and .map files from a .dose.vcf.gz file that I have gotten from Michigan's Imputation Server. I've tried the following command:

vcftools --gzvcf chr21.dose.vcf.gz --plink --out chr21.dose

but all I get is the following:

VCFtools - v0.1.13
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
        --gzvcf chr21.dose.vcf.gz
        --out chr21.dose
        --plink

Using zlib version: 1.2.3
Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.
After filtering, kept 2441 out of 2441 Individuals
Writing PLINK PED and MAP files ...
**Error:  Could not open temporary file.**

Can anyone please help me figure out how to generate these files?

PS: the chr21.dose.vcf.gz file also comes with the following files:

  • chr21.dose.vcf.gz.tbi
  • chr21.info.gz
gwas imputation
• 8,989 views • link
updated by Ram Ram • written by Diego.Morales • Diego.Morales

2 answers

I am not sure if your file is in dosage format or vcf format ! Assuming that you have a vcf file, you can straight away read with plink2 using --vcf argument and recode it ped and map files. If what you have is a dosage file, you convert it to plink format using gtool

• 0 views • link
updated by Ram Ram • written by Veera Veera

Then you can read it through plink2

• 0 views • link
written by Veera Veera

I had exactly the same question and just run into the DosageConvertor to convert dosage files (in VCF format) from Minimac3 to MaCH or PLINK. I haven't tried it yet but I will soon..

Good luck!

• 1 views • link
updated by Ram Ram • written by m.acostaherrera • m.acostaherrera

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