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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 pre-computed intensity data using likelihood-based model. |
| #** 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). |
| #** This method is sensitive to estimate low levels of contamination. | | #** This method is sensitive to estimate low levels of contamination. |
| #** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample. | | #** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample. |
| + | #* [[VICES]] jointly estimates contamination and its sources from genotyping array intensities. |
| + | #** Can be useful to determine where in the process contamination occurred and whether DNA can be salvaged from leftover DNA earlier in the genotyping pipeline, or to revise laboratory protocols. |
| | | |
| == History == | | == History == |
| * Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010) | | * Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010) |