IlluminaBeadArrayFiles

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

Generating GTC 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.

Build instructions

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

Installation instructions

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

python setup.py install

Dependencies

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

Example usage

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: #22

GTC File Format

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

Description of classes and objects in exposed in package

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

code2genotype

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

NC, AA, AB, and BB

Constants representing byte values for associated genotypes

GenotypeCalls

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

NormalizationTransform

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

ScannerData

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

BeadPoolManifest

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.

RefStrand, SourceStrand

Represents different strand conventions in manifest

BeadPoolManifest

Read information from a binary BPM file

LocusAggregate

Aggregate information across many samples for a given loci

ClusterFile

Read information from a binary EGT file

Compatibility

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

License

Copyright (c) 2020, Illumina All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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