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

Hi Jeremy Huang,   Have you had any luck using the FDR approach on FilterMutectCalls? Using f-score-beta to weed out false positives sounds reasonable for this use case. You mentioned you were prev...

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• Emil Furat
• November 22, 2021 22:23
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1. Community
2. Somatic
3. Called Somatic Mutations High Frequency of C>A SNVs

Hi Jeremy Huang,   Thanks for providing us with that information! I talked to a member of our engineering team, and it looks like you are running the orientation bias filter correctly. Would you be...

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• Emil Furat
• November 15, 2021 17:42
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1. Community
2. General Discussion
3. DetermineGermlineContigPloidy

Hi faramarzg,   We appreciate you taking the time to explain your solution to this issue! If you have any other questions please let us know.   Kind regards, Emil

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• Emil Furat
• November 10, 2021 18:35
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3. Called Somatic Mutations High Frequency of C>A SNVs

Hi Jeremy Huang,   Thanks for reaching out. You mentioned that you attempted to port the WDL workflows for RNA SNV/indel calling, would you be able to confirm you have done so successfully?  The re...

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• Emil Furat
• November 08, 2021 22:02
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2. General Discussion
3. DetermineGermlineContigPloidy

Hi faramarzg,   I believe that the documentation you are looking for is the following: https://gatk.broadinstitute.org/hc/en-us/articles/360035531152--How-to-Call-common-and-rare-germline-copy-numb...

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• Emil Furat
• November 04, 2021 18:06
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