Vcftools In Java, Particularly Vcf-Compare

Question

[User 9906]

Hi,

Is there a JAVA implementation of vcftools . I am looking for vcf-compare particularly.

I have to modify vcf-compare and add new features but I am a java programmer and I wanted an open source code base to start on. ( My project will be open source too ) .

Thanks. Ashwin

Answer 1

[Juliofdiaz]

I wonder if Picard includes vcftools http://picard.sourceforge.net/index.shtml

[mylons]

picard has no support for VCF. GATK does though, and here's a decent example showing how to use it to diff 2 files: https://github.com/broadgsa/gatk/blob/master/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java

https://github.com/broadgsa/gatk

Answer 2

[mylons]

This might be worth looking at: https://github.com/broadgsa/gatk/blob/master/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java