Samuel Lee
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Activity overview
Latest activity by Samuel Lee-
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...
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Samuel Lee commented,
Hi rahelp, You should not be collecting allelic counts at every site contained in your preprocessed intervals. Rather, you should provide a (typically much smaller) set of common variant sites as i...
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Samuel Lee commented,
Hi Tintest, Thanks for your question. The depth parameter is defined so that the expected number of reads in each bin is, roughly, depth x systematic bias in the bin x copy number in the bin. This ...
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Samuel Lee commented,
Thanks. I will take a look at using packages compiled against OpenBLAS for the next iteration of the environment and will update here when I can.
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Samuel Lee commented,
I wonder if this may be an issue with numpy 1.17.5, which we updated to in the 4.1.8.0 Docker/conda changes. See https://numpy.org/doc/1.17/release.html: "Downstream developers should use Cython >=...
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Samuel Lee commented,
Hi WangZiwei, I don't think using the bam outs from HC/M2 would be necessary. It's unlikely that the pileup counts would be affected in a way that the ModelSegments noise model could not handle.
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Samuel Lee commented,
Hi jejacobs23, That cutoff should be fine. If you search around a bit, you'll find that we've variously used cutoffs of ~10% and ~2% in the common SNP lists we distribute in the resource package. Y...