VCFTools not filtering out biallelic sites

Question

[Alexander Skates]

I have some VCF files I'm trying to run through Haploview to calculate pairwise LD scores (I also need LOD scores, which is why I'm not simply using VCFTools for this), however I get the error "More than two alleles at marker XX" for a number of the files, as Haploview only works for biallelic markers.

I've tried to filter them out using:

./vcftools --gzvcf tmp/vcf/EURchr3.vcf.gz --min-alleles 2 --max-alleles 2

However although it appears to run successfully, I still get the error with Haploview.

Also, I'd like to keep the markers rather than simply filtering them out if possible...

Answer 1

[Alexander Skates]

./vcftools --gzvcf tmp/vcf/EURchr3.vcf.gz --min-alleles 2 --max-alleles 2 --recode --stdout | ./bgzip -c > tmp.vcf/filtered_EURchr3.vcf.gz

seems to do the job!