Question: GaTK reverse select interval list
0
gravatar for Niek De Klein
2.9 years ago by
Niek De Klein2.5k
Netherlands
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 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?

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 https://gatkforums.broadinstitute.org/gatk/? The GATK team is usually very helpful.

ADD REPLYlink written 2.9 years ago by olavur100
2
gravatar for Pierre Lindenbaum
2.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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

ADD COMMENTlink written 2.9 years ago by Pierre Lindenbaum129k
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