no genotypes in HWE report in PLINK from genomestudio output · Biostar

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no genotypes in HWE report in PLINK from genomestudio output

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

snp exome plink genotype

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written 10.3 years ago by sreyag.2891 •

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