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6.5 years ago
manimozhi26
•
0
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'
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.