I am trying to use the mutect2 multi-sample feature. As it is relatively new, I didn't find many documents about it. Would you please help to clarify a few questions?
1. If I understand it correctly, multi-sample feature is designed for multi-samples from the same patient. So inputted tumor samples were called against all inputted normal samples. There is no "matched-normal" to each tumor sample.
2. I tried to do mutect2 separately (Tumor 1 vs Normal 1, Tumor 2 vs Normal 2) or multi-sample (Tumor1 and Tumor2, vs Normal 1 and Normal 2 in one run). The result (vcf before filtering) is different. Some variants were only identified in multi-sample results, not in any of the separate results. May I know why?
3. If Point 1 is true, I am thinking that if multi-sample feature can be used in multi-samples from different patients? Seems it is possible to do so? The only issue is no "matched-normal" for tumor in each patient. But if we think any variant identified in normal samples should be excluded in somatic mutation, I think it is OK to use it for multi-samples from different patients?
4. If Point 3 is not right, what is the best way to combine mutect2 results from different patients if running separately? Seems like CombineVariants in GATK3 is a solution but it is not available in GATK4?
5. Related question. The MuTect2 Wdl in (https://github.com/broadinstitute/gatk/blob/master/scripts/mutect2_wdl/) is not very correct. (1) gatk_jar is defined as /root/gatk.jar, but in fact in gatk docker image it is /gatk/gatk.jar. (2) the mutect2_multi_sample.wdl is not multi-sample as discussed in Point 1. It just run multiple separate MuTect2 (one MuTect2 for each Tumor/Normal pair), not running one multi-sample MuTect2 for all samples.
Thanks for your time and answers on this.
Please sign in to leave a comment.