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Illumina / BeadArrayFiles

Python library to parse file formats related to Illumina bead arrays
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Determining log r ratio and b allele frequency #2

Closed palijmath closed 7 years ago

palijmath commented 7 years ago

Can this program be used to determine log r ratios and b allele frequencies? I have a set of .gtc files from an Illumina BeadChip run, and their corresponding manifest file in .bpm format. I’m interested in determining the log r ratios and b allele frequencies for each SNP, but when I use the applicable GenotypeCalls functions those values are returned as zeroes. I see how to use the NormalizationTransform functions to get the normalized x and y values, and the R and theta values from those. What would be the recommended next steps to obtain the log r ratios and b allele frequencies?

KelleyRyanM commented 7 years ago

Do you have access to the original IDAT files used to generate these GTC files? I believe the AutoConvert 2.0 version software will populate these fields when creating the GTC file.