R code that reproduces variant filtering of whole exome sequencing data of non-matched chroroid plexus tumors.
Thomas C, Soschinski P, Zwaig M, Oikonomopoulos S, Okonechnikov K, Pajtler KW, Sill M, Schweizer L, Koch A, Neumann J, Schüller U, Sahm F, Rauschenbach L, Keyvani K, Proescholdt M, Riemenschneider MJ, Segewiß J, Ruckert C, Grauer O, Monoranu CM, Lamszus K, Patrizi A, Kordes U, Siebert R, Kool M, Ragoussis J, Foulkes WD, Paulus W, Rivera B, Hasselblatt M. The genetic landscape of choroid plexus tumors in children and adults. Neuro Oncol. 2021 Apr 12;23(4):650-660. doi: 10.1093/neuonc/noaa267. PMID: 33249490; PMCID: PMC8041331.
Filter_Variants.R takes variants called by appreci8 and annotations from CancerVar as input.