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Test-drive the GATK tools and Best Practices pipelines on Terra
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Reverse select interval list
I have a file with RNA editing sites which I want to remove from my VCF. I can select all the RNA editing sites with:
java GenomeAnalysisTK.jar \ -T SelectVariants \ -R human_g1k_v37.fasta \ -V input.gg.vcf.gz \ -o output.gg.vcf.gz \ -L Human_AG_all_hg19_v2.intervals
but how can I select every SNP that is not in Human_AG_all_hg19_v2.intervals? Is there something like -invertSelect but for interval lists?