Somatic Hotspot mutation is filtered although evident with IGV
Answered
Hi all
I can't find evidence of key mutations after Mutect2 (Tumor-Normal Mode with PoN). On the other hand, I do see the mutation with IGV and i don't know why it was filtered.
For example,
patient 1:
6 Alt Allele (7%) in Normal and 42Alt allele(22%) in the tumor at a specific loci
patient 2:
1 Alt Allele (1%) in Normal & 140 Alt Allele (63%) in Tumor
patient 3:
0 Alt Allele (0%) in Normal & 32 Alt Allele (15%) in Tumor
Then the same site in the panel of Normals file appears as 4%
"BETA=8.51,65.65;FRACTION=0.041"
Question -
Is the filtering done based on presence of alt allele in the matched Normal samples or
2. is the filtering being carried out based on the "FRACTION=0.041" in the PON file?
workflow used was:
https://dockstore.org/workflows/github.com/broadinstitute/gatk/mutect2:4.1.6.0?tab=info
Thanks in advance
-
Official comment
Hi sahuno,
Sites that appear in the PON are blacklisted and rejected from analysis in order to remove technical artifacts. You can change this behavior with the --genotype-pon-sites argument.
We have some documentation and other forum posts describing this behavior:
- https://gatk.broadinstitute.org/hc/en-us/community/posts/360075855412-How-mutect2-panel-of-normal-works-
- https://gatk.broadinstitute.org/hc/en-us/community/posts/360077287611-Mutect2-panel-of-normals-design
- FAQ for Mutect2
- Mutect2 paper
Let me know if you have further questions.
Best,
Genevieve
Comment actions -
Hi sahuno,
I am going to move your post into our Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Genevieve
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