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Question #238
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Here some things I look first: #230 (comment) with a bit of experience, looking at the BAF plot quickly shows you if it looks good. |
Thank you for your advice and quick response. |
Really depends what you need. We sequence thousands of samples each year and don't go through them. Some cancer types such as lung are more difficult than others due to high amounts of sub-clonal alterations, but PureCN should pick the correct solution in vast majority of cases (>90%). When purity is low it's biased towards low ploidy, with high noise towards high ploidy. For mutation analysis, you need to double check since it's highly sensitive to wrong purity/ploidy. No way around unfortunately (and what everybody using those algorithms, ABSOLUTE, ASCAT,..., does). Mutation analysis is tricky in low purity and/or noisy samples, so you could filter for purity > 35-40% and log ratio standard deviation < 0.25 or so. |
Thanks. |
Hi,
May I ask you for some advice, in cases when I see that the selected model by pureCN is off e.g, lower purity than expected or mutations expected to be clonal are subclonal, or in tricky samples like FFPE, or lower coverage...
What are the most important parameters from the output that I should consider when selecting a new model that would fit more? GoF?
Thank you.
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