Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

CalculateContamination Sample Source

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    Genevieve Brandt (she/her)

    gufran it's not possible using only CalculateContamination. CalculateContamination looks for systematic deviation from a binomial distribution in reads at common HET sites. Like you wrote above, it outputs a contamination percentage which represents contamination from any source, not just other samples.

    If you want to find which sample is the contamination source, you can use IdentifyContaminant to extract a fingerprint of the contaminating sample. You can then use CrossCheckFingerprint to compare fingerprints to each other and determine the source of the contamination.

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