TCGAbiolinks maf files RAS mutation rate not matching maf files from firehose
0
0
Entering edit mode
tangming2005 ▴ 200
@tangming2005-6754
Last seen 9 weeks ago
United States

Hi,

I downloaded maf files by TCGAbiolinks

coad.mutect.maf <- GDCquery_Maf("COAD", pipelines = "mutect")
coad.mutect.maf %>% summarise(n_distinct(Tumor_Sample_Barcode))

#435
coad.mutect.maf %>% filter(Hugo_Symbol == "KRAS") %>% summarise(n_distinct(Tumor_Sample_Barcode))

#39

only 39/435 samples have KRAS mutation,

However, if I downloaded from firehose http://firebrowse.org/?cohort=COAD&download_dialog=true

around half the samples have KRAS mutations. so what's the difference?

#total

~/Downloads/gdac.broadinstitute.org_COAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0$ ls -1 *txt | wc -l
368

# with KRAS mutation

~/Downloads/gdac.broadinstitute.org_COAD.Mutation_Packager_Raw_Calls.Level_3.2016012800.0.0$ grep -l KRAS *txt | wc -l
176

 

TCGAbiolinks • 2.1k views
ADD COMMENT
0
Entering edit mode

One difference is GDCquery_Maf is accessing data aligned to hg38 while the one in firehose was aligned to hg19.

 

ADD REPLY
0
Entering edit mode

can I get the old hg19 data? but even it is aligned to hg38, the difference is just too big.

ADD REPLY
0
Entering edit mode
Hi,

Yes you can download MAF aligned to hg19, but it is not in the manual, I'm adding it.

https://gist.github.com/tiagochst/03f5a11aa45d67940d65c8dd9bc90a70

Yes, the difference is really big! 

From GDC Faqs

Why might variants found in TCGA-generated MAFs be missing from the GDC open access MAF files?

Some of the reasons particular mutations may have been removed include updates to third party databases, more conservative germline-masking rules by the GDC, and different mutation calling pipelines and versions. Despite these differences, the GDC recaptures over 97% of TCGA-validated variants in the controlled-access MAF files. The GDC suggests using controlled-access MAF files if important variants cannot be found in somatic MAF files.

ADD REPLY

Login before adding your answer.

Traffic: 479 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6