heterozygosity control from NGS data
Hi all,
We select 100 SNPs with MAF>0.3 based on gnomAD data, in order to determine whether the sample has been contaminated or not.
We found several samples with large rate of heterozygote, with low GATK contamination value.
Since the snps is selected with large MAFs, it is supposed that heterozygosity of the sample should not exceed a specific value.
My question is how to determine the cutoff of the heterozygosity rate? And is it reasonable to set up this control?
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