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snp microarray data analysis

Hello!

I have .bpm file generated from with Illumina human coreExome cheap. I am trying to simply identify gender based on SNP's captured on Y chromosome and look at allele frequency to do so. Below are the histograms of allele frequency of SNP's on Y chromosome for male and female samples.

The question is why there is so huge amount of SNPs with allele frequency ranging from 0.1 to 0.9 in female sample. Is this reason of contamination or what? And can someone link the best practice of .bpm files interpreting (cause this is all I have from this experiment)

array illumina snp
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updated by Ram Ram • written by Max Ivon Max Ivon

Not sure if I got the goal of the experiment. Didn't you expect to detect none snps on chromosome y in female samples? If you find something on chromosome y (or better, if you find chromosome y) in female samples it cannot be, regardless snps allelic frequency, only a problem of contamination? Correct if I am wrong please.

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updated by Ram Ram • written by Nicola Casiraghi Nicola Casiraghi

I've expected to find SNP on Y chromosome in female. The problem is that there are too many SNPs with allele frequency higher 0.1 than I've expected. So I'm not sure if it should be so or there is an error in experiment or interpretation or I don't get the meaning of allele frequency right.

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updated by Ram Ram • written by Max Ivon Max Ivon

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