Question: no genotypes in HWE report in PLINK from genomestudio output
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4.1 years ago by
sreyag.28910 wrote:

Hi, I am analysing a dataset of 306 samples of exome beadchip data(Illumina) . The GenomeStudio report has been generated in ped and map format for PLINK analysis. After generating a HWE report in PLINK, I noticed that the Y chromosome SNP probes show 0/0/0 in the GENO column. What could be the reason for this? None of the other non-autosomal SNPs show this. The clustering of the said probes was fine in GenomeStudio, and the call frequency for all probes was greater than 95%. -Sreya

genotype snp plink exome • 1.0k views
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