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3. Called Somatic Mutations High Frequency of C>A SNVs

Dear Emil, Thank you for the reply. I will definitely try the FilterMutectCalls using the FDR approach. I was wondering also if I could tune the --f-score-beta to being 0.5 or something like that t...

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• Jeremy Huang
• November 15, 2021 19:29
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3. Called Somatic Mutations High Frequency of C>A SNVs

Thank you for your response: This is my call to our slurm. The overabundance of the C>A or G>T i detect could be an ob-prior problem. It is supposed to auto-detect the C>A, G>T oxog artifacts but i...

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• Jeremy Huang
• November 12, 2021 06:57
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3. How do I ensure sequence context-dependent artifacts, such as for FFPE deamination, are filtered using the current version of GATK?

I'm having similar problems. I have a high-proportion of G>T and C>A calls in my vcf even after filtering and specifying ob-priors

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• Jeremy Huang
• November 11, 2021 21:43
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3. Called Somatic Mutations High Frequency of C>A SNVs

Since these were run on Novaseq, it could be Oxog oxidative artifact but shouldn't it be filtered with the ob-priors argument? G/T artifact Output of filtering.stats.   #<METADATA>Ln prior of delet...

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• Jeremy Huang
• November 10, 2021 17:57
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