When creating VCF files with bcftools I can obtain only the variant positions using -v option. But when I have a VCF file with all postions and I want to filter only for the ones with variations, which is the most appropiate option in vcftools?
I could do
bcftools -Scvg allpositions.vcf.gz > only_variants.vcf
But recalling the SNVs and genotypes seems a waste of CPU cycles to me.
I am not sure if it would be better to use any of these options in vcftools:
--non-ref-ac <float> --max-non-ref-ac <float> Include only sites with all Non-Reference Allele Counts within the specified range.
--min-alleles <int> --max-alleles <int> Include only sites with a number of alleles within the specified range. For example, to include only bi-allelic sites, one could use: vcftools --vcf file1.vcf --min-alleles 2 --max-alleles 2
Any help would be appreciated, and sorry if this has been asked before but I am not finding an answer for it.