GaTK 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? There is an -invertSelect but this only works for selection criteria of -select, is there something similar for interval lists?
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updated
by
Pierre Lindenbaum
•
written
by
Niek De Klein
•
written
by
Niek De Klein
1 answer
use
--excludeIntervals / -XL
One or more genomic intervals to exclude from processing
with --filterNotInMask and --maskName NOT_IN_BED --mask your.bed
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Pierre Lindenbaum
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Have you tried asking on https://gatkforums.broadinstitute.org/gatk/? The GATK team is usually very helpful.