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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?

(cross-post https://www.biostars.org/p/270811/)

Best Answer


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