Gannon Cottone
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Activity overview
Latest activity by Gannon Cottone-
Gannon Cottone created a post,
Determining Optimal Number of Samples to include in Panel of Normal
AnsweredHello, We have been following tutorial(s) 11682 and 11683 for sensitive detection of copy ratio alterations in benign tissue utilizing the PON sensitivity in place of a matched normal when one may ...
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Gannon Cottone created a post,
Sensitive Copy Ratio Pipeline compatibility with tool "mergeLevels"
Can you please provide a) GATK version used b) Exact GATK commands used c) The entire error log if applicable. Hello, my group and I are new to this field. I have been following tutorial(s) 11682 a...
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Gannon Cottone commented,
Hello Bhanu, I apologize as I did not submit my response last week. To answer your points: 1) All samples, case and PON, were sequenced using the same target kit and methods. 2) The samples in the...
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Gannon Cottone commented,
Hello Bhanu, No problem! I will only post two of the 20 otherwise my computer freezes up for some reason. Only 6 of the 20 look like sample #160. Thank you for your help!
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Gannon Cottone created a post,
Somatic copy ratio alterations in benign case samples
GATK 4.1.0 Hello I have been following tutorial(s) 11682 and 11683 for sensitive detection of copy ratio alterations in benign tissue. Previously we have used other tools, such as Mutect2, to look...