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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Suggestion for running compile_pfb.pl with 8K samples #37

Closed npatel22526 closed 5 years ago

npatel22526 commented 5 years ago

Hello Dr. Wang,

I have about 8K intensity files and it takes quite a long for generating PFB files with all 8K samples. I am planning to try two different approaches to generate PFB files faster

  1. Split SNP position files into 100 parts and run in parallel using argument '-snpposfile'
  2. Run with small number (2K or 4K) of intensity files

Does either of the above will significantly effect results or have any obvious downside that I am not considering ?

Best, Nick

kaichop commented 5 years ago

You only need to use 1k files, that would be good enough. -Kai

On Tue, Feb 26, 2019 at 10:44 AM Nihir notifications@github.com wrote:

Hello Dr. Wang,

I have about 8K intensity files and it takes quite a long for generating PFB files with all 8k samples. I am planning to try two different approaches to generate PFB files faster

  1. Split SNP position files into 100 parts and run in parallel using argument '-snpposfile'
  2. Run with small number (2K or 4K) of intensity files

Does either of the above will significantly effect results or have any obvious downside that I am not considering ?

Best, Nick

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npatel22526 commented 5 years ago

Thanks for clarification.