Allele-specific copy number analysis of tumors
In R:
Install FACETS:
install.packages("devtools")
devtools::install_github("mskcc/pctGCdata")
devtools::install_github("mskcc/facets", build_vignettes = TRUE)Then run the example script facets_example.R
Generate FACETS input from your own bam files using the script here:
https://github.com/mskcc/facets/tree/master/inst/extcode
