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Old 07-09-2014, 05:45 AM   #1
CowGirl
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Location: Switzerland

Join Date: Mar 2013
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Default Vcftools output in "012" format is empty

Hi everyone,
I've been trying to get vcftools to alter my vcf files (97 samples, around 1,000,000 variants) into matrix format, however the ".012" file is always empty .
The other files (FILENAME.012.indv, FILENAME.012.pos) are fine (i.e. the IDs of the 97 are listed in FILENAME.012.indv and the variant positions are listed in FILENAME.012.pos). There is no error message, and the log file looks good.

Here's my command line:
vcftools --gzvcf TEST.vcf.gz --012 --out TEST

I did notice that there are 97 emtpy lines in the FILENAME.012 file, coinciding with the number of samples I've got in my original .vcf file.

When I try this with the --plink option, I don't get any output either, but the --plink-tped seems to work fine.

Any ideas whats going on here and how I can get my .vcf file into 0 1 2 format?

Help very much appreciated,
Chris
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Old 07-09-2014, 12:24 PM   #2
chrchang
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If a slightly different format is ok (main body is 012, but marker/sample IDs are saved differently), try

plink --vcf TEST.vcf.gz --recode A --out TEST

(this requires plink 1.9)
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Old 07-10-2014, 12:24 AM   #3
CowGirl
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Hi Chrchang,

super, thanks for the tip!

Works like a charm, but I had to include "--cow" to adjust the number of chromosomes PLINK should read.

It would still be good to know whats happening with the vcftools results - anyone have an idea whats going on there? And why there's no error message?

Thanks,
Chris

Last edited by CowGirl; 07-10-2014 at 12:27 AM.
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