<p>Hi all,</p>

<p>The current version of MAF is 2.4. Does MuSiC support this or has any issues with this version, if we make a mutation file that conforms to its specification?</p>

<p>Are all of the MAF columns required? If not, which ones can be excluded and is the ordering of the columns important?</p>

<p>Many thanks in advance.</p>

Nope, to both questions.

The changes from MAF v2.3 to v2.4 are [detailed here][1]. Of the columns that MuSiC cares about, only `Variant_Classification` has some changes - the values `De_novo_Start_InFrame` and `De_novo_Start_OutOfFrame` are no longer allowed. But MuSiC still treats them as valid values for backward compatibility (see [this line of code][2]).

The order of the first 34 MAF columns is important. But only the following columns are actually used by the tools in MuSiC, while the others can be left blank, or can contain gibberish. `Hugo_Symbol`, `Chromosome`, `Start_position`, `End_position`, `Variant_Classification`, `Variant_Type`, `Reference_Allele`, `Tumor_Seq_Allele1`, `Tumor_Seq_Allele2`, `Tumor_Sample_Barcode`

Some tools in MuSiC require additional non-standard columns in the MAF (ordering doesn't matter, as long as they're after column 34). For example, the tools `cosmic` and `proximity` need the MAF to specify the `transcript_name` (doesn't matter what convention as long as its consistent), `amino_acid_change`([protein change in HGVS][3]), and `c_position`([codon change in HGVS][4]) that each variant was annotated to.

 [1]: https://wiki.nci.nih.gov/pages/viewpage.action?pageId=26187384
 [2]: https://github.com/genome/gms-core/blob/master/lib/perl/Genome/Model/Tools/Music/Bmr/CalcBmr.pm#L363
 [3]: http://www.hgvs.org/mutnomen/recs-prot.html
 [4]: http://www.hgvs.org/mutnomen/recs-DNA.html