Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

VariantFiltration PASSing the variants with missing values

Hi,
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?

Thanks,
~N

Best Answer

Answers

Sign In or Register to comment.