This pipeline runs Copykat and adds a subsequent calling step that can call chromosome arm level alterations in individual cells
Mandatory parameters
Rscript copykat_pipeline.R
-c [counts matrix]
-g [chromosome coordinates]
-o [output directory]
Recommended parameters - maually specify which cells to use as completely normal
-l [File with aneuploid/diploid labels per cell with column names cell.names
(barcodes) and copykat.pred (diploid or aneuploid)]
Optional parameters for additional plots
-u [UMAP coordinates (colnames UMAP_1 and UMAP_2), with further possible annotations
of columns named cluster and/or celltype]
The pipeline has been tested with R version 4.1.1
optparse
copykat
tidyr
gtools
ggplot2
cowplot