gatk SelectVariants -R reference.fasta -V input.vcf -select-type SNP -O snps.vcf
conda install -c bioconda bcftools
Editing a 500GB VCF? Use these strategies: vcf edit
This long-form guide explores everything you need to know about VCF editing, from simple manual fixes for individual files to advanced software solutions for batch processing thousands of contacts. gatk SelectVariants -R reference
provide tools to view or convert these files, while specialized online VCF editors allow you to upload, modify, and download the updated version. Raw Text Editing: vcf edit