I'm using GATK version4. After using VariantFiltration, I got the information of "PASS" of "not PASS". Next I want to filter out the "not PASS" variants. So I used the Selectvariants but, I can't filtered out the the not PASS variant well?
Please tell me how to use the -select argument.
Thank you
codes are as below
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hkmac2017:exome_bam hirokikimura$ java -jar /Users/hirokikimura/exome_bam/gatk-4.1.2-2.0/gatk-package-4.1.2.0-local.jar SelectVariants -R human_g1k_v37_decoy.fasta -V combined_genotyped_filtered_snps_indels_mixed.vcf -select "FILTER == PASS" -O combined_genotyped_filtered_snps_indels_mixed.PASS.vcf
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Please tell me how to use the -select argument.
Thank you
codes are as below
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hkmac2017:exome_bam hirokikimura$ java -jar /Users/hirokikimura/exome_bam/gatk-4.1.2-2.0/gatk-package-4.1.2.0-local.jar SelectVariants -R human_g1k_v37_decoy.fasta -V combined_genotyped_filtered_snps_indels_mixed.vcf -select "FILTER == PASS" -O combined_genotyped_filtered_snps_indels_mixed.PASS.vcf
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