hhall.hg18.pfb and hhall.hg18.gcmodel files not available

[aydzhouyuan]

Dear Kai

I am currently processing a pretty old dataset from Human670-QuadCustom_v1_A array. I first tried to generate the pfb file using my own data (~270 healthy samples and ~ 10K cases). I found the average number of rare CNV (frequency < 1%) for individuals is much higher comparing with UKBB dataset.

I suspect this maybe due to the fact that the dataset is skewed as most are cases, that would influence the pfb file?

I then tired to use the hhall.hg18.pfb and hhall.hg18.gcmodel as Human670 is similar to Human610, from this website: http://penncnv.openbioinformatics.org/en/latest/misc/faq/. it appeared that these files are in the pennyCNV package.

However, when I downloaded all the pennCNV (1.0.0-1.0.5) from the GitHub. either hhall.hg18.pfb or hhall.hg18.gcmodel are not in the lib folder.

Any idea why and are you able to share these two files?

Thank you and I am looking forward to hearing from you soon.

Yuan

[kaichop]

You will need to build the PFB file yourself. Essentially they contains the BAF values for these markers. You can use compile_pfb.pl program to generate this file from your own input files.

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On Mon, Dec 7, 2020 at 8:25 PM aydzhouyuan ***@***.***> wrote: Dear Kai I am currently processing a pretty old dataset from Human670-QuadCustom_v1_A array. I first tried to generate the pfb file using my own data (~270 healthy samples and ~ 10K cases). I found the average number of rare CNV (frequency < 1%) for individuals is much higher comparing with UKBB dataset. I suspect this maybe due to the fact that the dataset is skewed as most are cases, that would influence the pfb file? I then tired to use the hhall.hg18.pfb and hhall.hg18.gcmodel as Human670 is similar to Human610, from this website: http://penncnv.openbioinformatics.org/en/latest/misc/faq/. it appeared that these files are in the pennyCNV package. However, when I downloaded all the pennCNV (1.0.0-1.0.5) from the GitHub. either hhall.hg18.pfb or hhall.hg18.gcmodel are not in the lib folder. Any idea why and are you able to share these two files? Thank you and I am looking forward to hearing from you soon. Yuan — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#63>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OBEQRGXOX4BEXNKIETSTV6BZANCNFSM4URIMEYA> .

[aydzhouyuan]

Thank you for much for your reply. do I use the healthy samples only or all the samples to generate the pfb file? would that influence the CNV calling?

[kaichop]

From empirical experience, it does not really matter much. If you have more samples, it is fine to combine them together to generate the file.

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On Tue, Dec 8, 2020 at 4:37 AM aydzhouyuan ***@***.***> wrote: Thank you for much for your reply. do I use the healthy samples only or all the samples to generate the pfb file? would that influence the CNV calling? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#63 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OH4LHTX4G5PV2RECA3STXXVZANCNFSM4URIMEYA> .