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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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qcnumcnv #70

Closed psychrb closed 3 years ago

psychrb commented 3 years ago

For filter.cnv.pl: 1) What is the default for qcnumcnv without inserting a flag..? If this flag is not added, is there any filtering..? 2) This is the maximum number of cnv's/sample for inclusion in filtered output, correct?.. So if qcnumcnv 80 is inserted, a sample with more than 80 will be excluded, correct?

kaichop commented 3 years ago

If it is not specified, then the filter is not used. The number depends on the array, and is typically selected by researchers themselves based on extreme value that are observed in a specific data set, to exclude some samples from analysis.

On Tue, Mar 2, 2021 at 10:55 AM psychrb notifications@github.com wrote:

For filter.cnv.pl:

  1. What is the default for qcnumcnv without inserting a flag..? If this flag is not added, is there any filtering..?
  2. This is the maximum number of cnv's/sample for inclusion in filtered output, correct?.. So if qcnumcnv 80 is inserted, a sample with more than 80 will be excluded, correct?

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