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VariantFiltration PASSing the variants with missing values

I am running VariantFiltration (GATK v 3.4) using the following command:

java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg19.fa -V raw_snps.vcf --filterExpression "QUAL/DP < 2.0 || DP < 10.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 4.0" --missingValuesInExpressionsShouldEvaluateAsFailing --filterName "current" -o filtered_snps.vcf

Only half of the variants have the MQRankSum values and in spite of having the argument '--missingValuesInExpressionsShouldEvaluateAsFailing', the output file has many variants marked as PASS that do not have MQRankSum. Ideally, the ones without MQRankSum annotation should not be marked as PASS, right? Is this a bug issue?

Also, on the side, how do get GATK to remove the variants from the file that do not PASS. So, only have the PASS variants in the output file?


Best Answer


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