Tcga Mutation Data File

Question

[kanwarjag]

I downloaded a TCGA mutation data file (broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2) which has mutation data in it it has extension of Access short cut

I tried to open in Access it is not opening saying it is not correct format.

Any one suggest how I can open this file other files like manifest etc are txt files and open well.

Thanks

[Neilfws]

Would help to provide a link to the file or directory or at least the complete file name.

I guess you are on Windows. Don't be.

Presumably the file extension is ".mdb", which Windows thinks is an Access database file. Clearly, it is not. I'd guess it's something to do with MDB-seq data.

UPDATE: now we know that the extension is .maf, see answer from Chris.

[kanwarjag]

yes that is correct I was on windows. While I looked in shell- it is Unix Executable File, full name is broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2.maf I will still need pointers how to extract data Thanks

[Pierre Lindenbaum]

try to use the file command to detect the real format of your file http://linux.die.net/man/1/file

Answer 1

[Chris Miller]

What you downloaded is a MAF file, which is simply tab-delimited text. It can be opened and manipulated using a plethora of command-line utilities. If you're really feeling masochistic, you can even use a spreadsheet program like excel, but watch out for quirks like gene-renaming. (http://www.ncbi.nlm.nih.gov/pubmed/15214961)

The MAF format is documented here: https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification

[ajay nair]

The MAF format is no longer available in the given link. New link is: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/