How To Calculate Maf From Tcga Data?

Question

[liu4gre]

which dataset and which level should be used? Is it possible to get it from level2 dnaseq data? or SNP data?

Answer 1

[Chris Miller]

To clarify, are you asking about minor allele frequency or mutation annotation format?

If the latter, MAF (format) files are part of the level 2 mutation data for each cancer type.

If the former, some MAF (format) files contain readcounts and variant allele frequency information, but it's an optional appended field, IIRC. For those MAF files that lack readcount data, you'd have to pull down the bams and generate that information yourself. You might also look in the VCF files, which I think contain that information.

If you're looking for the global minor allele frequency, you'll need to cross-reference sites from the MAFs or VCFs with population data from dbSNP, 1000 genomes project, or exome variant server.

[liu4gre]

Thanks. I am looking for minor allele frequency

Answer 2

[Charles Warden]

I think you should check out this post:

Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)

[liu4gre]

Thanks for the info. Actually I have read the post, but still didnot get how to calculate MAF ...

[Charles Warden]

If you still have questions, I would recommend asking them as comments on that other post. Perhaps someone who is part of the TCGA team can help.