Supplementary Figure 2: A panel-of-normals strategy is effective in removing germline variants and recurrent technical artifacts. | Nature Biotechnology

Supplementary Figure 2: A panel-of-normals strategy is effective in removing germline variants and recurrent technical artifacts.

From: Accurate detection of mosaic variants in sequencing data without matched controls

Supplementary Figure 2

(a) Among the variants present in the PoNs, 82.3% were present in ≥3 individuals, and thus, are most likely to be technical artefacts or common variants. Furthermore, although 17.7% of the recurrent variants were only called twice by MuTect2 in the 75 individuals, about half of them have ≥3 alt alleles in ≥3 individuals (checked using samtools mpileup), indicating that these are most likely artefacts. (b) The MosaicForecast-Refine model trained with our brain WGS data was applied to call mosaics from the MuTect2 call set (using data from three individuals with single cell sequencing data available), different variant filtering strategies were used, including not using a panel-of-normals (left), filtering variants called in >2 samples (middle) and filtering variants called in ≥2 individuals. Variants called were evaluated using single cell sequencing data and IonTorrent data. Removing recurrent variants does not result in the loss of any true variants, and the validation rate was ~10% higher.

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