Question: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
0
gravatar for -_-
19 months ago by
-_-720
Canada
-_-720 wrote:

I am looking at this http://firebrowse.org/, KICH, Mutation Annotation File, and I downloaded both

  • Mutation_Packager_Calls (MD5)
  • Mutation_Packager_Oncotated_Calls (MD5)

But I only found MAF files for tumour samples, and couldn't find the corresponding MAFs file for normal samples. Any idea where they could be?

Also, what's the difference between the mutations in these two files, please?

ADD COMMENTlink modified 29 days ago by Wenhu_Cao50 • written 19 months ago by -_-720

Have you known the differences between this two files yet?

ADD REPLYlink written 29 days ago by Wenhu_Cao50

Not really. But I think the later is filtered is oncotator somehow

ADD REPLYlink written 28 days ago by -_-720

Not really. But I think the later is filtered is oncotator somehow

ADD REPLYlink written 28 days ago by -_-720

Yeah, I also think so.

ADD REPLYlink written 28 days ago by Wenhu_Cao50
1
gravatar for Chris Miller
9 weeks ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

Those are somatic mutations and are all called in the tumor samples relative to the normal. Germline mutations are protected with an additional level of restrictions, but are available, but almost certainly in VCF, not MAF format.

ADD COMMENTlink written 9 weeks ago by Chris Miller20k

Thanks for the insight! Also, how could I know if they are called from genome or just exome data. I am mainly interested in mutations in non-coding regions.

ADD REPLYlink written 9 weeks ago by -_-720

I got it, it's in Sequence_Source column. But I found it's all WXS for 993 BRCA MAF files. Where could I find MAF for whole-genome sequencing data, please?

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by -_-720

Some tumors have it, some don't. To the best of my knowledge, the GDC (https://portal.gdc.cancer.gov/) is currently the canonical source for TCGA data.

ADD REPLYlink written 9 weeks ago by Chris Miller20k
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