GaTK reverse select interval list
1
0
Entering edit mode
6.7 years ago
Niek De Klein ★ 2.6k

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?

GATK intervallist • 2.0k views
ADD COMMENT
0
Entering edit mode

Have you tried asking on https://gatkforums.broadinstitute.org/gatk/? The GATK team is usually very helpful.

ADD REPLY

Login before adding your answer.

Traffic: 2188 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6