genotype call for probe

[cmccabe0728]

Is this the genotype of the probe or the reference? I believe it is the probe.... is there a way to add the reference genotype to it? Thank you.

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

[jzieve]

It is the probe. Adding the reference requires mapping to the reference genome (essentially calling the variant, i.e., outputting a VCF). I would recommend using DRAGEN Array for that purpose, specifically the gtc-to-vcf feature: https://help.dragenarray.illumina.com/product-guides/dragen-array-local-analysis#genotype-gtc-to-vcf You can also use the open source, python version of that here: https://github.com/Illumina/GTCtoVCF but that is no longer actively maintained.