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Different amount of unfiltered variants when using different PON's


I'm analyzing the impact of two different panel of normals on the final results in tumor-only mode with Mutect2
I found out that the vcf files on these two analyses differ in the amount of unfiltered variants. I didn't expect this, because the panel of normals is also used in the filter steps later on to indicate variants as non-somatic (FilterMutectCalls). I also checked what happens when I don't use a panel of normals at all. These are the results:
pon A: 53958 variants
pon B: 50768 variants
No pon: 121485 variants

The only difference in these analyses are the panel of normals. Other settings are kept the same.
My question is: why does it seems that the panel of normals has impact on both the amount of unfiltered variants as on the filtersteps in FilterMutectCalls?


Best Answer


  • Erik84Erik84 Member

    Hi Shlee,

    Thank you very much for your reply. Now I understand what is happening. :smile:


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