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
Your must have
For generic HD parameter see hd-params.md.
Specific to this data type is the following:
ERRORfor failing when encountering a probability not summing up to one.
WARNfor 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.
|region_name||Mandatory The name of this region. Often it's a gene name. e.g.
||Optional log2 ratio of the measurement.|
||Optional Segmented log2 ratio.|
||Optional Actual probability of homologous loss.|
||Optional Actual probability of loss.|
||Optional Actual probability of normal.|
||Optional Actual probability of gain.|
||Optional Actual probability of amplification.|