Error:VCF version must be v4.0 or v4.1:

Question

[zwang10]

I ran

vcftools --gzvcf raw_variants.vcf.gz --freq --chr 1 --out chr1_analysis

But I got

VCFtools - v0.1.11
(C) Adam Auton 2009

Parameters as interpreted:
    --gzvcf raw_variants.vcf.gz
    --chr 1
    --freq
    --out chr1_analysis

Using zlib version: 1.2.8
Index file is older than variant file. Will regenerate.
Building new index file.
Error:VCF version must be v4.0 or v4.1:
You are using version VCFv4.2

I did not find vcf version 4.0 or 4.1

Answer 1

[Pierre Lindenbaum]

your VCFTools is just too old and only recognizes the old VCF formats.