Mutect2 - Joint calling
Answered
Hello, I have a question about the tumor with matched normal. I used the mutect2 to call variant from single tumor and single normal (I had the three tumor samples, so I run three times). After filtering, annotation and merge. And I ran another way that is joint calling of multiple tumor and one normal sample. But I found that some variants in first way (Single tumor and single normal) could not be found in variants from joint calling.
Is joint calling stricter than single pair calling?
Thank you,
Yen-Ping Yeh
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Hi Yen-Ping Yeh,
Joint calling is not possible with our best practices pipelines so we do not have any information about this.
You can read more about somatic variant calling here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890491
And our best practices pipeline here: https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels-
Best,
Genevieve
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Yen-Ping Yeh Mutect2 multisample mode is only intended for multiple tumor samples from the same person. Is that the case here?
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Yeah, there are four samples (three tumors and one normal) from the same patient.
Thanks for your response. -
Yen-Ping Yeh Multi-sample mode is usually more sensitive because it is able to call variants that have mediocre evidence in several samples. However, it can be less sensitive in the case where only one sample has a variant and the evidence in that sample is barely sufficient. In such a case the preponderance of non-variant reads in the other samples dilutes the signal.
To some extent this is mathematically appropriate, because seeing several samples without a variant should make you less confident. However, our multisample genotyping is definitely not as sophisticated as it could be and the dilution effect I mentioned above would be weaker with a more rigorous model.
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I'm sorry for responding it late. Thank you for your answer. Finally, I still used two modes (single and multiple mode) to get vcf from Mutect2. It is just like you said Multi-sample mode diluted the signal, so there are some variants not being found with multi-sample mode.
Thank you very much.
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David Benjamin: Does that mean if we use multisample mode, we should use it with multi-site samples of 1 tumor, not with different time samples like diagnostic VS recurrent?
Thank you
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Hi Joe Doasi,
Yes, multi-sample mode should be used with multiple samples from the same tumor as Mutect2 will genotype all reads jointly.
Best,
Pamela
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Joe Doasi You may also use multisample mode with a time series. The important thing is that all samples must come from the same person: multiple sites of one tumor, time series, primary tumor and metastases etc. From a technical point of view, the important thing is that the germline variation is identical among all tumor samples.
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