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

Question

[Diego.Morales]

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

Answer 1

[Veera]

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

[Veera]

Then you can read it through plink2

[Diego.Morales]

It looks like a VCF file

Answer 2

[m.acostaherrera]

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!