VCFTOOLS won't read my vcf file

Question

[wruzic1]

I'm having trouble getting vcftools to read my vcf file generated from snp array genotyping with the Illumina InfiniumOmniExpressExome-8v1-6_A1 beadarray. I'm using vcftools newly installed and up to date on Ubuntu running on my windows 10 machine.

When I run the command vcftools --vcf B4072.vcf I get the following output:

Parameters as interpreted: --vcf B4072.vcf

After filtering, kept 0 out of 0 Individuals Duplicate alternate alleles found at N)+:0 Duplicate alternate alleles found at /`@*:0

I'm able to load and view the contents of this file using vcfR, and can see the data is present for my 956298 variants. Can anyone help me understand what I'm doing wrong?

Thanks, Brad

[Pierre Lindenbaum]

you'd better use bcftools;

what is the output of

file  B4072.vcf

Answer 1

[wruzic1]

Thanks for your help and sorry to clog up the board. Found my error - I actually have .gcf.gz files - my windows machine dropped the .gz before I pushed them over to my ubuntu installation. Thanks, Brad