I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Just follow some of the steps that I use here for your VCF: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format

Specifically:

• Convert the 1000 Genomes files to BCF
• Convert the BCF files to PLINK format

To help, here's the code to use:

#1st pipe, splits multi-allelic calls into separate variant calls
#2nd pipe, left-aligns indels and issues warnings when the REF base in your VCF does not match the base in the supplied FASTA reference genome
bcftools norm -m-any MyVariants.vcf.gz | bcftools norm -Ob --check-ref w -f /ReferenceMaterial/1000Genomes/human_g1k_v37.fasta > MyVariants.bcf ;

bcftools index MyVariants.bcf ;

plink --noweb --bcf MyVariants.bcf --keep-allele-order --vcf-idspace-to _ --const-fid --allow-extra-chr 0 --split-x b37 no-fail --make-bed --out MyVariants ;

Once you get it into PED format, then do your filtering for MAF, etc.

Kevin