Vcftools output in "012" format is empty

[CowGirl]

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

[chrchang]

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)

[CowGirl]

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