VCFtools error

Question

[Sammy]

Hiya,

I ran vcftools --vcf file.vcf --freq and vcftools --vcf file.vcf --plink and I get the same error:

> VCFtools - 0.1.15
(C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted:
    --vcf file.vcf
    --freq
Error:VCF version must be v4.0, v4.1 or v4.2:
You are using version VCFv4.2 ##fileformat=VCFv4.2 ##fileformat=VCFv4.2

It looks strange to me, I don't understand what's the issue, is it the the VCF in front of v4.2 (in ##fileformat=VCFv4.2) that causes the confusion?

Thanks!

[4galaxy77]

vcftools is very old and no longer under development. If you want to estimate allele frequencies, plink2 is the best choice, and it natively reads vcfs without needing conversion.

[Sammy]

Thanks, the output from plink returned something like:

chr | rs code | ref allele | alt allele | MAF |no. alleles

which is great! But some rs codes are . and don't know what variants it's referring to. Looking for alternative ways to get the MAFs with the positions as well so I can identify them! Also looking for options in plink. Thanks!

Plink2 returns AF now and I need MAF, trying to work around that.

[Ram]

Why did you delete your post, Sammy?

[Sammy]

It seemed irrelevant :)

[Ram]

You had the question and received feedback, adding knowledge to the community. It is not irrelevant, it is a record of learning.

[Sammy]

Got it, thanks!