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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Compile pfb Bovine data #86

Closed rodrigopsav closed 2 years ago

rodrigopsav commented 2 years ago

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 commented 2 years ago

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.

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

  1. Is there any flag to change the maximum number of autosomes?

Thanks, Rodrigo

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rodrigopsav commented 2 years ago

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.