Question: GaTK reverse select interval list
gravatar for Niek De Klein
2.9 years ago by
Niek De Klein2.5k
Niek De Klein2.5k wrote:

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 \
    -o \
    -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?

intervallist gatk • 1.0k views
ADD COMMENTlink modified 2.9 years ago by Pierre Lindenbaum129k • written 2.9 years ago by Niek De Klein2.5k

Have you tried asking on The GATK team is usually very helpful.

ADD REPLYlink written 2.9 years ago by olavur100
gravatar for Pierre Lindenbaum
2.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:


--excludeIntervals / -XL

One or more genomic intervals to exclude from processing

with --filterNotInMask and --maskName NOT_IN_BED --mask your.bed

ADD COMMENTlink written 2.9 years ago by Pierre Lindenbaum129k
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