That's a good idea. I was concerned that v4.3 might be too different from 4.2 but you are right, I should at least just try to change the version number in the vcf file and see if that works. Thank you! I will post an update if that works.

The sed command you suggested worked for the analyses I needed. Thank you again for your help!

I know it's been a long time since you answered but maybe you can still help me. I have the same issue but this does not seem to work for me. What am I doing wrong?

First I do this like you suggested:

LC_ALL=C sed 's/^##fileformat=VCFv4.3/##fileformat=VCFv4.2/' ALL.chr.vcf.gz > newALL.chr.vcf.gz

And then this again:

vcftools --gzvcf newALL.chr.vcf.gz --snps chr.csv --recode --out filtered_output  

Which again gives me the error

Error: VCF version must be v4.0, v4.1 or v4.2: You are using version VCFv4.3

I would be very grateful for help!