GaTK reverse select interval list

Question

[Niek De Klein]

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?

[olavur]

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

Answer 1

[Pierre Lindenbaum]

use

https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_engine_CommandLineGATK.php#--excludeIntervals

--excludeIntervals / -XL

One or more genomic intervals to exclude from processing

https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php

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