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CalculateContamination on non-tumour samples

I have seen that calculate contamination is part of a somatic workflow but is there any reason that it cannot be used on germline samples to detect potential contamination (in tumor-only mode?).
Apologies if this has been answered elsewhere. I wasn't able to find anything when I looked.


  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @sararar You may use CalculateContamination in tumor-only mode as you described on a germline sample. However, since it's a cancer tool that needs to work well even in a sample with lots of copy-number variation it is very cautious about ploidy. Germline contamination tools generally assume the sample is diploid, which adds power when it's true. I wouldn't worry about this if it's much more convenient to use CalculateContamination but I also don't want to give the impression that we have replaced tools like VerifyBamID, at least not until we set up an evaluation that shows this.

  • sarararsararar Member
    Thank you. We have been using verifybamid, however it is showing high levels of contamination in most of the samples we run on an Illumina NextSeq. As it is not likely that all of the samples on several runs are contaminated I am looking for another tool.
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