CalculateContamination Sample Source

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gufran

• November 25, 2020 15:30
• Edited

Hello

I have been wondering if there is any way that I could find contamination source. I am using CalculateContamination but it only gives contamination percentage. Is there any way I can find which sample does contamination come from.

If it is not possible, can I get a bam file with reads which counted as contaminated. Even a text file which has read IDs.

Thanks in advance

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  Genevieve Brandt (she/her)

  • November 30, 2020 22:35

  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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