Get MAF files aligned against hg19

maf_legacy.R

query.maf.hg19 <- GDCquery(project = "TCGA-COAD", 
                           data.category = "Simple nucleotide variation", 
                           data.type = "Simple somatic mutation",
                           access = "open", 
                           legacy = TRUE)
# Check maf availables
knitr::kable(getResults(query.maf.hg19)[,c("created_datetime","file_name")]) 

query.maf.hg19 <- GDCquery(project = "TCGA-COAD", 
                           data.category = "Simple nucleotide variation", 
                           data.type = "Simple somatic mutation",
                           access = "open", 
                           file.type = "gsc_COAD_pairs.aggregated.capture.tcga.uuid.automated.somatic.maf",
                           legacy = TRUE)
GDCdownload(query.maf.hg19)
coad.mutect.maf <- GDCprepare(query.maf.hg19)

library(dplyr)
coad.mutect.maf %>% summarise(n_distinct(Tumor_Sample_Barcode))
coad.mutect.maf %>% filter(Hugo_Symbol == "KRAS") %>% summarise(n_distinct(Tumor_Sample_Barcode))

indeed, the old hg19 has more KRAS mutations.
Thanks for looking into this.

Tommy