Samuel Lee
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Activity overview
Latest activity by Samuel Lee-
Samuel Lee commented,
Zhuo Xm thanks for sharing the file. I think you will want to adjust the neutral-segment-copy-ratio-lower-bound and neutral-segment-copy-ratio-upper-bound parameters; these set the bounds of the co...
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Samuel Lee commented,
Zhuo Xm still no luck. Feel free to email the file to slee AT broadinstitute.org if that's easier.
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Samuel Lee commented,
Hi Zhuo Xm, Thanks, I can see the file, but the file size is zero. I think the file did not upload correctly (as the last line of your log would suggest). Can you try again? -rw-r--r-- 1 ebanks wg...
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Samuel Lee commented,
Thanks Zhuo Xm, I think you can find instructions for the FTP at https://gatk.broadinstitute.org/hc/en-us/articles/360035889671
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Samuel Lee commented,
Hi Zhuo Xm, Would it be possible to share the command lines and input files for the CallCopyRatioSegments runs on both the problematic sample (2322_S5_110) and a non-problematic one? We'd want to s...
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Samuel Lee commented,
Hi Lindo Nkambule, Just wanted to follow up with you as well. To clarify Genevieve's comment, when setting that particular parameter to 75, that means you are only retaining 1 out of every 75 varia...
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Samuel Lee commented,
Hi Anjali Kumari, Can you provide more information about the input intervals given by hg38.interval_list? If I understand correctly, your 67M interval_list.tsv output corresponds to these input int...
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Samuel Lee commented,
Thanks everyone for contributing to this thread! Just to make sure this doesn't get lost in the shuffle---if you use -L to run this tool just over common variant sites (typically around ~1-10M site...
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Samuel Lee commented,
Hi Tintest, If I understand correctly, you want to determine which of the two models should be used with incoming samples in case mode? One approach we've used in the past is to use a simple "precl...
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Samuel Lee commented,
Hi Tintest Yes, this parameter is basically supposed to represent overall depth. If your model fits are both good across the two cohorts, you could reasonably compare the distributions of this para...