Fail to apply --filterExpression to raw vcf file when running VariantFiltration

liuxingliangliuxingliang SingaporeMember

Hi all,

I tried to apply the following command to my raw vcf file to filter it using the filtering expression specified in the command:

java -XX:ConcGCThreads=4 -XX:+UseConcMarkSweepGC -XX:ParallelGCThreads=4 -jar GenomeAnalysisTK.jar -T VariantFiltration -R human_g1k_v37.fa --variant human_g1k_v37.CHL124.vcf_snps.vcf -o CHL124.vcf_snps.vcf_filter_marked.vcf --filterExpression "QD < 2.0 && MQ < 40.0 && FS > 60.0 && HaplotypeScore > 13.0 && MQRankSum < -12.5 && ReadPosRankSum < -8.0" --filterName "very_small_SNPs_default_filter"

After that, I check my result file which is CHL124.vcf_snps.vcf_filter_marked.vcf, I found that, all reads are marked as "PASS" whether its QD is > 2.0 or < 2.0. Obviously, the command doesn't work, but I cannot find why everything seems goes well, no error reported.


Best Answer


  • liuxingliangliuxingliang SingaporeMember

    thanks a lot, after checking the meaning of each flag, yes, each one should be filtered, so I should use OR instead of AND, thx Kurt, have a nice day:)

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