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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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PennCNV-Affy for Genome-wide 6.0 #49

Closed Taylor95 closed 4 years ago

Taylor95 commented 4 years ago

Hello, I am trying to call CNVs from Genome-wide 6.0 array and it has data of 906,600 SNPs and 946,000 CN probes. I wonder what is the calling based on, SNPs or CN probes? In .rawcnv, startsnp and endsnp contain both SNPs and CN probes. Can PennCNV-Affy package call CNVs just based on CN probes?

And, I found the BAF value of CN probes are all 2 in individual signal file, could this affect the calling CNVs? The following is a example of individual signal file :

CN_496308 1 836746 0.3908 2 CN_522419 1 818586 -0.1996 2 CN_489691 1 824136 0.3437 2

Thanks in advance!

kaichop commented 4 years ago

BAF=2 means that there is no BAF (it is not a SNP marker)

On Fri, Nov 15, 2019 at 3:42 AM Taylor95 notifications@github.com wrote:

Hello, I am trying to call CNVs from Genome-wide 6.0 array and it has data of 906,600 SNPs and 946,000 CN probes. I wonder what is the calling based on, SNPs or CN probes? In .rawcnv, startsnp and endsnp contain both SNPs and CN probes. Can PennCNV-Affy package call CNVs just based on CN probes?

And, I found the BAF value of CN probes are all 2 in individual signal file:

CN_496308 1 836746 0.3908 2 CN_522419 1 818586 -0.1996 2 CN_489691 1 824136 0.3437 2

Thanks in advance!

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Taylor95 commented 4 years ago

So, if I want to call CNVs based on CN probes, I just need to remove SNP markers? How will it deal since both PFB and BAF value are 2?

kaichop commented 4 years ago

No, you do not need to do anything. PennCNV can call CNV using both SNP markers and CN markers.

On Mon, Nov 18, 2019 at 8:07 PM Taylor95 notifications@github.com wrote:

So, if I want to call CNVs based on CN probes, I just need to remove SNP markers? How will it deal since both PFB and BAF value are 2?

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