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Hi, Is there any update on the Mutect2 pipeline for liquid biopsy or even the CLIA-approved liquid biopsy pipeline ? Best, Ying

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• yingchen69
• April 21, 2022 02:23
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1. Community
2. Special GATK Use Cases
3. Mutec2 - Liquid Biopsy

Hi, Is there any update on the Mutect2 pipeline for liquid biopsy or even the CLIA-approved liquid biopsy pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360055062832-New-Year-update-GA...

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• yingchen69
• April 21, 2022 02:10
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2. Somatic
3. Mutect2 missing a low AF known deletion

Hi Genevieve, Actually it passed the filtering which is a surprise to me. chr17 7577542 . TCATGCCGCC T . PASS AS_FilterStatus=SITE;AS_SB_TABLE=10519,11258|256,292;DP=22325;ECNT=1;GERMQ=93;MBQ=20,20...

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• yingchen69
• January 14, 2022 18:47
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1. Community
2. Somatic
3. Mutect2 missing a low AF known deletion

Hi Genevieve, Thanks a lot for the suggestion. I ran the tests with the site chr17:7577542 added to the force calling site list and all test runs called the 9 base deletion with AF 0.025 no matter ...

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• yingchen69
• January 14, 2022 17:16
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