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#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.
#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.
# When a sample has array-based genotypes but not yet sequenced
# When a sample has array-based genotypes but not yet sequenced
#* [[VerifyIntensity]] software can estimate the levels of DNA sample contamination from aligned sequence reads and population allele frequency
#* [[VerifyIDintensity]] software can estimate the levels of DNA sample contamination from aligned sequence reads and population allele frequency
#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone
#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone
#** [[VerifyIntensity]] models array intensity data instead of sequence reads
#** [[VerifyIDintensity]] models array intensity data instead of sequence reads
#** When a large number of samples are genotyped together, the 'multi-sample' option will estimate the intensity distribution for each marker across multiple samples. When only one a few samples are genotyped, 'per-sample' option will estimate the intensity distribution for each sample across all markers.
#** When a large number of samples are genotyped together, the 'multi-sample' option will estimate the intensity distribution for each marker across multiple samples. When only one a few samples are genotyped, 'per-sample' option will estimate the intensity distribution for each sample across all markers.
#* [[BAFRegress]] software can estimate levels of sample contamination and test the presence of contamination by regressing the allele frequency with respect to the B allele frequency (BAF).
#* [[BAFRegress]] software can estimate levels of sample contamination and test the presence of contamination by regressing the allele frequency with respect to the B allele frequency (BAF).
