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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Confidence score calculation #103

Open sherrybio opened 1 year ago

sherrybio commented 1 year ago

Hi Dr. Wang,

I want to find out PennCNV confidence score to filter the number of CNVs in our Autism spectrum disorder project but I do not any resources for that. I have found all the papers related to confidence score used in PennCNV but they do not have specific programs or instructions that I can follow. Therefore, I want to ask if you can help me solve this problem?

I am looking forward to your response.

Thank you, Sherry

kaichop commented 1 year ago

It is better to just use number of SNPs and length of CNV calls as a threshold. The problem with confidence score is that it is less comparable across samples (i.e. it can tell whether some calls are more confident than others in the same sample, but the same scoring scale is not comparable across samples when there is strong heterogeneity of quality of different samples in a cohort). Using the number of SNPs and length of CNV calls is better in the sense that the same criteria can be applied to all samples.

On Wed, Mar 8, 2023 at 5:27 PM sherrybio @.***> wrote:

Hi Dr. Wang,

I want to find out PennCNV confidence score to filter the number of CNVs in our Autism spectrum disorder project but I do not any resources for that. I have found all the papers related to confidence score used in PennCNV but they do not have specific programs or instructions that I can follow. Therefore, I want to ask if you can help me solve this problem?

I am looking forward to your response.

Thank you, Sherry

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