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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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custom pfb - duplicate values #43

Closed andrisvAria closed 5 years ago

andrisvAria commented 5 years ago

Hey,

I am trying to create my own pfb for Illumina GSA. I compiled the pfb using 500 samples. The output is quite big and I noticed that there are a lot of duplicates, with different baf values. How should I deal with the duplicates? Do they somehow affect the next step detect_cnv? Can I remove them?

image

kaichop commented 5 years ago

This should not occur. Are they the exact same SNP? Did you check that these duplicates are in the original input files (same location, but different SNP identifiers?) -Kai

On Tue, May 28, 2019 at 7:32 AM andri90 notifications@github.com wrote:

Hey,

I am trying to create my own pfb for Illumina GSA. I compiled the pfb using 500 samples. The output is quite big and I noticed that there are a lot of duplicates, with different baf values. How should I deal with the duplicates? Do they somehow affect the next step detect_cnv? Can I remove them?

[image: image] https://user-images.githubusercontent.com/51119653/58474950-dc001000-814c-11e9-95b3-ac34a20fd87b.png

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andrisvAria commented 5 years ago

I doublechecked my procedure and found out it was due to a problem with splitting the original Illumina report that contained the samples. I now have a pfb file with unique values. Thank you

-Andri

kaichop commented 5 years ago

Okay thank you for the update.