Where are mutation files (MAF) for TCGA normal samples on Firebrowse

Question

[-_-]

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?

[Wenhu_Cao]

Have you known the differences between this two files yet?

[-_-]

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

[-_-]

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

[Wenhu_Cao]

Yeah, I also think so.

Answer 1

[Chris Miller]

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.

[-_-]

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.

[-_-]

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?

[Chris Miller]

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.