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SelectVariant from FILTER column
Dear GATK Team
I am wondering is there any option in GATK'S SelectVariants walker (I am quite sure that its the best as per my need) to select all those variants which have 'SnpCluster' record in the FILTER column. As I do not want those variants that have 'PASS' records.
I tried with this:
java -jar /home/wuk/software/GenomeAnalysisTK.jar -T SelectVariants -R /home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly38.fasta -V snp_clsters2_ws3.vcf -o snp_clsters2_ws3_clstronly.vcf -select "FILTER == 'SnpCluster'"
and many other combinations but I failed every time. What should be the best walker option or JEXL argument for that?