Samuel Lee
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Activity overview
Latest activity by Samuel Lee-
Samuel Lee commented,
Hi Weichi I think that if you further crank global-psi-scale down you should start to get the desired results. For example, I set it to 1E-6 (which is probably extreme), and this yielded ploidy = 1...
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Samuel Lee commented,
Hi Weichi, Thanks for these additional questions and test results! Apologies for the delay, I took some vacation over the past few days but will return to looking at this later today. The distribut...
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Samuel Lee commented,
Thanks Weichi! And oops, one more thing—can you share your intervals file?
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Samuel Lee commented,
Thanks Weichi! That data looks pretty clean, so I think we should be able to get a good result. Perhaps some hyperparameters might need to be adjusted? Would you mind sharing that samples-by-covera...
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Samuel Lee commented,
Yes, this file must be in TSV format. I was speaking very generally about Bayesian inference https://en.wikipedia.org/wiki/Bayesian_inference. If your inferences depend very sensitively on the part...
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Samuel Lee commented,
Yes, that should be fine for an initial run. As a general principle, if your analysis is sensitive to your priors, then your data is not very informative.
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Samuel Lee commented,
Your results should hopefully not be too sensitive to the particular values used in this table—they are just priors. Typically you would not need to construct a new table for each batch unless your...
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Samuel Lee commented,
You cannot skip this step. The contig-ploidy priors table is simply a resource file that is provided to the tool. You should only need to construct this file a single time---no need to automaticall...
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Samuel Lee commented,
Hi Weichi, Apologies that you are running into difficulties, but thank you for this very clear and informative report! The DetermineGermlineContigPloidy tool attempts to fit a very simple model tha...
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Samuel Lee commented,
Hi Y R, Take another look at the workflow diagram in the tutorial you linked. In cohort mode, the recommended steps would be: 1) PreprocessIntervals 2) AnnotateIntervals 3) CollectReadCounts 4) Fil...