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Old 11-04-2013, 11:26 PM   #2
Location: San Francisco, CA

Join Date: Mar 2012
Posts: 21

You can use the GATK VariantAnnotator .

So something like:

java -jar GenomeAnalysisTK.jar -T VariantAnnotator
-R mm9.fa
--variant input.vcf
--dbsnp dbsnp135_path.vcf
-A DepthPerAlleleBySample # you can run with --list to see other -A options
-resource:my_dbsnp,vcf dbsnp135_path.vcf -E my_dbsnp.infofieldname
-resource:my_snps2,vcf my_snps2_path.vcf -E my_snps2.infofiledname1 -E my_snps2.infofieldname2 -comp my_snps2, vcf my_snps2_path.vcf
-o output.vcf

This will produce output.vcf which has all the variants in input.vcf along with additional INFO field values based on values from the other .vcf files.
It should then be possible to use GATK SelectVariants (or some other filtering tool) to extract the variants that you want.

GATK tools can be somewhat complicated to use, so there's also this list:

Last edited by bw.; 11-04-2013 at 11:30 PM.
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