Compile pfb Bovine data

[rodrigopsav]

Hello,
I am using PennCNV for bovine data. I am using compile_pfb.pl to compile the pfb of my samples. However, it outputs only the pfb up to chromosome 23. Is there any flag to change the maximum number of autosomes?

Thanks,
Rodrigo

[kaichop]

It should not have this behavior since compile_pfb.pl does not check chromosome number. I suspect your original input file does not have chromosome over 23. If you are doing detect_cnv.pl then you can use -lastchr to denote the largest autosome. But again I do not think it is relevant to your question on compile_pfb.pl. You can check your input file to ensure that it has all the autosomes.

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On Fri, May 20, 2022 at 5:13 PM rodrigopsav ***@***.***> wrote: Hello, I am using PennCNV for bovine data. I am using compile_pfb.pl to compile the pfb of my samples. However, it outputs only the pfb up to chromosome 23. Is there any flag to change the maximum number of autosomes? Thanks, Rodrigo — Reply to this email directly, view it on GitHub <#86>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OCUX6U3IHAOYFO4D23VK76ADANCNFSM5WQTHFDQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[rodrigopsav]

Thanks for answering me. I figure out what was happening. The original input has all the chromosomes. Later on, I applied some quality control filters to remove bad data points (snps and samples) and that worked. It was just a coincidence that PennCNV was keeping data points up to chromosome 23.