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.
6 Alt Allele (7%) in Normal and 42Alt allele(22%) in the tumor at a specific loci
1 Alt Allele (1%) in Normal & 140 Alt Allele (63%) in Tumor
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%
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:
Thanks in advance
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