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cnv.md

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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

Uploading CNV data requires a cnv.params file.

For generic HD parameter see hd-params.md.

Specific to this data type is the following parameter:

  • 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.

Data file format

The first column 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 defined in your subject-sample mapping (e.g. CACO2). The columns that contain the copy number state probabilities are not required, but if present in a row, all these columns should be filled in.

Column Name Description
region_name (Mandatory) The name of this region as defined in your annotations file (e.g. WASH7P)
<sample_code>.flag (Mandatory) Copy number state of. Possible values are: -2 - homozygous loss, -1 - loss 0 - normal, 1 - gain, 2 - amplification.
<sample_code>.chip log2 ratio of the measurement.
<sample_code>.segmented Segmented log2 ratio.
<sample_code>.probhomloss Probability of homozygous loss.
<sample_code>.probloss Probability of loss.
<sample_code>.probnorm Probability of normal.
<sample_code>.probgain Probability of gain.
<sample_code>.probamp Probability of amplification.