CCLE maf files

[shwetha141]

Hi PoisonAlien, I am very very new to bioinformatics and I apologize if this is a dumb questions. Would it be possible to show how you can apply your tools to CCLE maf file? I tried separating the file to individual lineage maf files but having difficulty in running MutsigCV on them. I am sorry if I am not making sense. My question is that if you can apply your tool for CCLE maf file.

Thanks.

Shwetha

[PoisonAlien]

Hello,

Yes you can process any data as long as it complies to MAF format. Here is a snippet on how to generate CCLE maf object

#Download CCLE maf file (details here: https://depmap.org/portal/download/) 
download.file("https://ndownloader.figshare.com/files/34989940", destfile = "ccle.maf")
ccle = data.table::fread(file = "ccle.maf")
#Change some column names
tsb_idx = which(colnames(ccle) == "DepMap_ID")
tsa2_idx = which(colnames(ccle) == "Alternate_Allele")
colnames(ccle)[tsa2_idx] = "Tumor_Seq_Allele2"
colnames(ccle)[tsb_idx] = "Tumor_Sample_Barcode"

#Cell line annotations (DepMap ID to many..)
download.file("https://ndownloader.figshare.com/files/35020903", destfile = "ccle.clinicalInfo.csv")
sampinfo = data.table::fread(input = "ccle.clinicalInfo.csv")
colnames(sampinfo)[1] = "Tumor_Sample_Barcode"

#Make MAF
ccle = maftools::read.maf(maf = ccle, clinicalData = sampinfo)