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/)