To further reduce false positives and miscalled germline events, we employ a panel of normal samples as a filter. To create this filter we run MuTect on a set of normals as if they were tumors without a matched normal in STD mode. From this data, a VCF file is created for the sites that were identified as variant by MuTect in more than one normal.
This VCF is then supplied to the caller, which rejects these sites. However, if the site was present in the supplied VCF of known mutations (--cosmic) it is retained because these sites could represent known recurrent somatic mutations which have been detected in the panel of normal when the normal are from adjacent tissue or have some contamination tumor DNA.
The more normal samples used to construct this panel, the higher the power will be to detect and remove rare artifacts. Therefore, we typically we use all the normal samples readily available. The results presented here were obtained by using a panel of whole genome sequencing data from blood normals of 125 solid tumor cancer patients. The samples used as part of the virtual tumor approach were not included in this panel.
This VCF is then supplied to the caller, which rejects these sites. However, if the site was present in the supplied VCF of known mutations (--cosmic) it is retained because these sites could represent known recurrent somatic mutations which have been detected in the panel of normal when the normal are from adjacent tissue or have some contamination tumor DNA.
The more normal samples used to construct this panel, the higher the power will be to detect and remove rare artifacts. Therefore, we typically we use all the normal samples readily available. The results presented here were obtained by using a panel of whole genome sequencing data from blood normals of 125 solid tumor cancer patients. The samples used as part of the virtual tumor approach were not included in this panel.
