Library to parse binary file formats related to Illumina bead arrays. The IlluminaBeadArrayFiles library provides a parser to extract information from these binary files.

If you have intensity data files (IDATs) for which GTC files are not currently available, it is possible to generate these files using Illumina software. We recommend using DRAGEN Array.

The IlluminaBeadArrayFiles repository supports building a package with the python distutils module (https://docs.python.org/2/distutils/setupscript.html). To build a source distribution, run the included setup.py script supplying the "sdist" command

python setup.py sdist

After unpacking the installation package, run the setup.py script supplying the "install" command

python setup.py install

The library depends on the availability of the numpy package in the python installation (http://www.numpy.org/)

from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype

gtc_file = "path_to_genotypes.gtc"
manifest_file = "path_to_manifest.bpm"
names = BeadPoolManifest( manifest_file ).names
genotypes = GenotypeCalls( gtc_file ).get_genotypes()

c = 0  # a counter to only show the first 10 genotypes
for (locus, genotype) in zip( names, genotypes ):
    print( locus + "," + code2genotype[genotype] )
    if c >= 10:
        break
    c += 1

Also, see examples/* for additional examples of usage. These scripts are based on common Genome Studio (https://support.illumina.com/array/array_software/genomestudio.html) reports.

NOTE: For the DNA summary report, it does not exclude zeroed loci from the cluster file as it does in Genome Studio, so overall call rates may look lower. There is an open issue to address this: Illumina#22

The specification for the GTC file format is provided in docs/GTC_File_Format_v5.pdf

For further details on specific class methods, please consult the built-in docstring documentation

Dictionary mapping from genotype byte code (see GTC file format specification) to a string representing the genotype (e.g., "AA")

Constants representing byte values for associated genotypes

Class to parse GTC files as produced by Illumina AutoConvert and AutoCall software.

Class to encapsulate a normalization transform for conversion of raw intensity data to normalized intensity data

Class to encapsulate the meta-data collected in the GTC file for a scanner instrument

Class for parsing a binary (BPM) manifest file. This class can be used to recover the in-order list of loci names in a given manifest, which is necessary to associate the genotype information present in the GTC file to a specific locus name.

Represents different strand conventions in manifest

Read information from a binary BPM file

Aggregate information across many samples for a given loci

Read information from a binary EGT file

This library is compatible with Python 3 and was tested with Python 3.8.5

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