I using the function genotype.Illumina from CRLMM package to calls genotyping raw data files of an Illumina HumanOmni 2.5 SNP array.
g = genotype.Illumina(cdfName='humanomni25quadv1b', path=full_path_dir, call.method='krlmm') g_c = calls(g)
g_c has 2449907 (one for each SNP). But non of them seems to be a Mitochondrial SNP, even though the analyzed platform has 93 Mitochondrial SNPs. For example, MitoT217C which is also known as rs41531144 does not appear in the recalling object.
How can it be?