GATK has a tool "SelectVariants" that has some standard filter options and you can create filter expressions based on the attributes in the vcf records: http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html

You can also use SnpSift to build filter expressions on the standards vcf attributes and the ones added by SnpEff effect prediction: http://snpeff.sourceforge.net/SnpSift.html

http://www.bioconductor.org/packages/2.12/bioc/html/VariantAnnotation.html

vcf objects are basically sample-subsettable granges - a very clever implementation

If you want a quick and highly customizable way to filter vcfs, try perl one-liners.

perl -lne 'print $_ if ($_ =~ /0\/1/)' < my_vcf_file.vcf > filtered_vcf_file.vcf

will get you all the variants where the genotype has been called as "0/1". In English, this one-liner says "print the line if the line contains the string "0/1".

perl -lane 'print $F[5] if ($_ !~ /^#/)' < my_vcf_file.vcf > QUAL_scores.txt

will get you a list of all the QUAL scores. In English, this says "print the value in the sixth column if the line does not start with a # character".

My favorite perl one-liner guide is here. A one-liner is no replacement for a proper filtering script, but for getting a sense of the distribution of your data there's nothing better.

While it imports your VCF into a database first, our GEMINI software is specifically designed to allow filtering of variants in VCF files based on genome annotations and sample genotypes.

See Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations thread. Also, please see the documentation.

An example of a GEMINI query filtering variants based on allele frequency and functional impact:

$ gemini query -q "select * from variants \
                  where is_lof = 1 \
                  and aaf >= 0.01" my.db

Extend this to further filter based on sample Thelonius being a heterozygote

$ gemini query -q "select * from variants \
                  where is_lof = 1 \
                  and aaf >= 0.01" 
         --gt-filter "gt_types.Thelonius == HET" \
         my.db

Hi,

You can also look at the extension of Plink! that manages VCF files: http://atgu.mgh.harvard.edu/plinkseq/overview.shtml

Best

Filter using javascript: https://github.com/lindenb/jvarkit#-filtering-vcf-with-javascript-rhino-

/** prints a VARIATION if two samples at least
have a DP<200 */ 
function myfilterFunction()
    {
    var samples=header.genotypeSamples;
    var countOkDp=0;


    for(var i=0; i< samples.size();++i)
        {
        var sampleName=samples.get(i);
        if(! variant.hasGenotype(sampleName)) continue;
        var genotype = variant.genotypes.get(sampleName);
        if( ! genotype.hasDP()) continue;
        var dp= genotype.getDP();
        if(dp < 200 ) countOkDp++;
        }
    return (countOkDp>2)
    }
myfilterFunction();

.

$ gunzip -c file.vcf.gz |\
   java -jar  dist/vcffilterjs.jar  SCRIPT_FILE=filter.js

The snpSift package has snpSift filter operation that is quite powerful and performant.

http://snpeff.sourceforge.net/SnpSift.html#filter