The first 34 columns are standard MAF format, and described here:
https://wiki.nci.nih.gov/x/eJaPAQ

The subsequent 10 columns are relevant to most analyses:

35. HGVSc - the coding sequence of the variant in HGVS recommended format
36. HGVSp - the protein sequence of the variant in HGVS recommended format
37. Transcript_ID - transcript onto which the consequence of the variant has been mapped
38. Exon_Number - the exon number (out of total number)
39. t_depth - read depth across this locus in tumor BAM
40. t_ref_count - read depth supporting the reference allele in tumor BAM
41. t_alt_count - read depth supporting the variant allele in tumor BAM
42. n_depth - read depth across this locus in normal BAM
43. n_ref_count - read depth supporting the reference allele in normal BAM
44. n_alt_count - read depth supporting the variant allele in normal BAM

All remaining columns are straight out of the snpEff annotator, as described here:
http://snpeff.sourceforge.net/SnpEff_manual.html#output

45. Effect - Effect of variant. Details here: http://snpeff.sourceforge.net/SnpEff_manual.html#eff
46. Effect_Impact - Effect impact {High, Moderate, Low, Modifier}
47. Functional_Class - Functional class {NONE, SILENT, MISSENSE, NONSENSE}
48. Codon_Change - Old_codon/new_codon OR distance to transcript (for non-coding variants)
49. Amino_Acid_Change - Amino acid change: old_AA/AA_position/new_AA (e.g. 'E30K')
50. Amino_Acid_Length - Length of protein in amino acids (is actually transcription length divided by 3)
51. Gene_Name - Gene name, as per the transcript database used
52. Transcript_BioType - Transcript bioType, if available
53. Gene_Coding - [CODING | NON_CODING]. This field is 'CODING' if any transcript of the gene is marked as protein coding
54. Transcript_ID - Transcript ID (usually ENSEMBL IDs)
55. Exon_Rank - Exon rank or Intron rank (e.g. '1' for the first exon, '2' for the second exon, etc.)
56. Genotype_Number - Genotype number corresponding to this effect (e.g. '2' if the effect corresponds to the second ALT)
57. ERRORS - Any errors (not shown if empty)
58. WARNINGS - Any warnings (not shown if empty)

Add distributable readme for snpEff MAFs
Add distributable readme for snpEff MAFs
