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
Vcftools In Java, Particularly Vcf-Compare
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
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User 9906 •
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I wonder if Picard includes vcftools http://picard.sourceforge.net/index.shtml
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