Extracting information from gatk VariantFiltration output

Question

[zizigolu]

Hi

I am filtering by GATK VariantFiltration option and I need variant corresponding to PASS column in my output file , how I can extract only variant passed the filter?

This is my command

-bash-4.1$ java -jar /home/local/software/GATK/3.7/source/GenomeAnalysisTK.jar -T VariantFiltration -R ./hs37d5.fa -o somatic.snvs.vcf -V /somatic.snvs.vcf --filterExpression "AB < 0.2 || MQ0 > 50" --filterName ″HARD_TO_VALIDATE″^C
-bash-4.1$

Any help?

Answer 1

[zizigolu]

java -jar ./GenomeAnalysisTK.jar -T SelectVariants -R ./genome.fa -V ./snvs.vcf -ef -o ./selected.vcf