see the latest post on my blog:

"Reading/Writing a VCF file with the GATK-API. "

http://plindenbaum.blogspot.fr/2012/11/readingwriting-vcf-file-with-gatk-api.html

C++: vcflib

The design was meant to be similar to bamtools, which I found very easy to work with. You open a VCF file and iterate through record, populating an object with the VCF record on each iteration. You can write out VCF records using the << operator. Documentation is sparse, because I continuously develop the library as a way of dealing with edge cases not handled by by other systems such as vcf-tools or the GATK. Variant.h should provide ample self-documentation. Function names are meant to be self-explanatory.

Example usage, counting the number of alternate alleles in a VCF file (taken from vcfcountalleles):

#include "Variant.h"

using namespace std;
using namespace vcf;

int main(int argc, char** argv) {

    VariantCallFile variantFile;
    string filename = argv[1];
    variantFile.open(filename);

    int uniqueAlleles = 0;

    Variant var(variantFile);
    while (variantFile.getNextVariant(var)) {
        uniqueAlleles += var.alleles.size();
    }

    cout << uniqueAlleles << endl;

    return 0;

}

There are a lot of existing functions in the library for doing everything from haplotype-based allele intersection to filtering to genotype annotation. The stock programs in the library are almost entirely designed to read and write VCF, so, for instance, whenever possible annotations are added to records rather than dumped in a separate format, allowing the streaming of the results of one into the next and so on.

I intend to document them and will post a news item here on BioStar and also seqanswers when I do.

Python: https://github.com/jamescasbon/PyVCF

Have a look at the Perl API vcf.pm) from the VCFtools.

"VCFtools contains a Perl API Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc."