Help - GATK Variant filtration by AD/DP not working · Biostar

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Help - GATK Variant filtration by AD/DP not working

Hi everyone,

I am having trouble with this command. I have a vcf file with 100's of samples. And I want to apply sample level filter on allele frequency which is AD/DP. I have been trying it with this command but no luck. It marks all entries as filtered. When I simply tried with AD.0 >10, the command works as expected which tells me that it recognized AD.0 as number of reference reads. But somehow the division does not give me the right answer. Has anyone run into this issue?

java -jar GenomeAnalysisTK.jar -T VariantFiltration -R .ucsc_hg19.fa -V test.vcf -o test.vf.vcf -G_filter "(AD.0) / DP >0.8" --genotypeFilterName 'lowAD'

gatk variantfiltration filter vcf

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written 8.9 years ago by manimozhi26 0

Hello manimozhi26!

It appears that your post has been cross-posted to another site: https://gatkforums.broadinstitute.org/gatk/discussion/comment/43343#Comment_43343

This is typically not recommended as it runs the risk of annoying people in both communities.

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written 8.9 years ago by Pierre Lindenbaum 17K

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