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BaitBias Artifact Filter
Hi GATK team,
We recently have a set of targeted sequencing samples showing inflated G>T false positive variants. Picard CollectSequencingArtifactMetrics showed that almost all samples in the batch is having very low bait bias qscore(under 30) for G to T base change.
I read through the picard document about BaitBiasSummaryMetrics and PreAdapterSummaryMetrics. They used G>T example for both types of artifact. It gave me a not very clear impression that BaitBias is looking for bias between reference and complementary while PreAdapterSummaryMetrics is looking for an orientation bias?
Can I have a more understandable explanation of how to differentiate elevated G>T rates that are OxoG artifacts, or G-ref artifacts?
Also, GATK4 has an experimental tool FilterByOrientationBias(https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_exome_FilterByOrientationBias.php)
to filter out OxoG artifact. I'm wondering is there a similar tool that can potentially remove G-ref artifact given SequencingArtifactMetrics.BaitBiasDetailMetrics?