cnv.md

CNV

Platform Upload

Your platform configuration file has to have the cnv_annotation.params name. The content of the params file is the same as for other HD data types.

For format of the platform data file see chromosomal_region.md

CNV Data Upload

Your must have cnv.params file.

For generic HD parameter see hd-params.md.

Specific to this data type is the following:

• PROB_IS_NOT_1 Default: ERROR. ERROR for failing when encountering a probability not summing up to one. WARN for logging the error and continuing.

Below is the expected file format for CNV data input files. First column always has to be region name. The rest of the columns are recognised by the name, not by position. Replace <sample_code> with an actual sample code (e.g. CACO2).

Column Name	Description
region_name	Mandatory The name of this region. Often it's a gene name. e.g. WASH7P
<sample_code>.flag	Mandatory -2 - homologous loss, -1 - loss 0 - normal, 1 - gain, 2 - amplification.
<sample_code>.chip	Optional log2 ratio of the measurement.
<sample_code>.segmented	Optional Segmented log2 ratio.
<sample_code>.probhomloss	Optional Actual probability of homologous loss.
<sample_code>.probloss	Optional Actual probability of loss.
<sample_code>.probnorm	Optional Actual probability of normal.
<sample_code>.probgain	Optional Actual probability of gain.
<sample_code>.probamp	Optional Actual probability of amplification.