Affymetrix® Genotyping Console CHP Data File Format
CHP FILE
Description
The CHP files generated by the Genotyping Console software contain SNP analysis results from the Birdseed, BRLMM and Axiom™GT1 genotyping algorithms.
CNCHP and LOHCHP files containing Copy Number and Loss of Heterozygosity results generated by the Genotyping Console software are described in a separate document. CNVCHP files containing Copy Number Variation Results generated by the Genotyping Console software are also described in a separate document.
Format
The format of the CHP file generated by the Command Console software uses the Command Console binary data format. The following describes the data sets and groups stored in the file.
The parameters stored in the header of the file include algorithm parameters (those whose names are prefixed with "affymetrix-algorithm-parameter-") and summary statistics (those whose names are prefixed with "affymetrix-chipsummary-"). These parameters are algorithm specific.
SNP Results
The analysis results from the SNP algorithms are stored in a single group with a single data set. The data set header will contain a set of parameters to define the column labels.
The data type identifier is set to: "affymetrix-multi-data-type-analysis"
The data group containing the analysis results is called "MultiData".
For the SNP results, these are stored in a data set named "Genotype"
A data set generated by BRLMM or Birdseed contains the following columns:
| Column Name | Column Type |
|---|---|
| ProbeSetName | Ascii |
| Call | UByte (6 = AA, 7 = BB, 8 = AB, no call otherwise) |
| Confidence | Float |
| ForcedCall | UByte (6 = AA, 7 = BB, 8 = AB) |
| SignalA+ | Float |
| SignalB+ | Float |
| Contrast* | Float |
| Strength* | Float |
+ The signal A and B values are stored for the Birdseed algorithms.
* The contrast and strength values are stored for the BRLMM algorithm.
A data set generated by the Axiom™GT1 algorithm contains the following columns:
| Column Name | Column Type |
|---|---|
| ProbeSetName | Ascii |
| Call | UByte (6 = AA, 7 = BB, 8 = AB, no call otherwise) |
| Confidence | Float |
| Log Ratio | Float |
| Strength | Float |
| ForcedCall | UByte (6 = AA, 7 = BB, 8 = AB) |