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?
• 2,619 views
•
link
1 answer
use
--excludeIntervals / -XL
One or more genomic intervals to exclude from processing
with --filterNotInMask and --maskName NOT_IN_BED --mask your.bed
• 0 views
•
link
Log in to answer this question.
Have you tried asking on https://gatkforums.broadinstitute.org/gatk/? The GATK team is usually very helpful.