Contamination
Estimate sample contamination.
Introduction
Two metrics are used to estimate sample contamination: minor contamination and major contamination. Moreover, minor contamination is calculated separately for collapsed and duplex BAMs. Both contamination metrics are produced by the fingerprinting SNP set. However, minor contamination is calculated using just the homozygous sites, whereas the major contamination is via the ratio of heterozygous to homozygous sites. For each contamination-BAM type combination there is a table showing per-sample contamination values and any associated metrics.
Methods
Tool used: biometrics BAM type: (1) collapsed BAM and (2) duplex BAM Regions: MSK-ACCESS-v1_0-curatedSNPs.vcf
It is a two step process to produce the table: (1) extract SNP genotypes from each sample using biometrics extract command and (2) perform a pairwise comparison of all samples to determine sample relatedness using the biometrics minor and biometrics major commands. Please see the biometrics documentation for further documentation on the methods.
Interpretation
Minor contamination
Samples with minor contamination rates of >0.002 are considered contamination.
Major contamination
The fraction of heterozygous positions should be around 0.5. If the fraction is greater than 0.6, it is considered to have major contamination.
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