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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Unexpectedly high log2 ratios for some but not all samples #700

Open zetamui opened 2 years ago

zetamui commented 2 years ago

I have tried to compare the samples with or without this issue but couldn't find anything that could be the reason. Apart from ploidy # are there other reasons that could contribute to this unexpected high observed log2 ratio?

Best, Zeta

etal commented 2 years ago

Are the high log2 ratios in the bin-level data (.cnr files) or segments (.cnr files)? Were the ratios high for all data points, or just a few? If you can post a scatter plot here, that would be helpful to triage your issue.

zetamui commented 2 years ago

This is a sample with normal values (most values close to 0): Normal_1 The cnr log2 values density: Normal_1_cnr_log2_ratio_density The cns log2 values density: Normal_1_cns_log2_ratio_density

All of these samples below have unexpected higher ratios (some not as high as others)

This sample named Abnormal 3 has an average of 2.79: Abnormal_3

The cnr log2 values density: Abnormal_3_cnr_log2_ratio_density The cns log2 values density: Abnormal_3_cns_log2_ratio_density

This sample named Abnormal 2 has an average of 0.72: Abnormal_2

The cnr log2 value density: Abnormal_2_cnr_log2_ratio_density The cns log2 value density Abnormal_2_cns_log2_ratio_density

This sample named Abnormal 4 has an average of 1.28: Abnormal_4 The cnr log2 values density: Abnormal_4_cnr_log2_ratio_density The cns log2 values density: Abnormal_4_cns_log2_ratio_density

This sample named Abnormal 1 has an average of 0.85: Abnormal_1

The cnr log2 values density: Abnormal_1_cnr_log2_ratio_density The cns log2 values density: Abnormal_1_cns_log2_ratio_density

Thank you so much for your patience!