Bayesian haplotype-based genetic polymorphism discovery and genotyping.
freebayes
VCFtools is a program package designed for working with VCF files
vcf-annotate vcf-fix-newlines vcf-query vcf-to-tab vcf-compare vcf-fix-ploidy vcf-shuffle-cols vcf-tstv vcf-concat vcf-indel-stats vcf-sort vcfutils.pl vcf-consensus vcf-isec vcf-stats vcf-validator vcf-contrast vcf-merge vcf-subset vcf-convert vcf-phased-join vcftools