Information on fields in the pipeline's MAF output

[sorelfitzgibbon]

• The output maf has 133 fields of which 28 are non-blank. These are listed below, many are not helpful. Where specific text is given the field in invariant.
• Looks like their may be a vcf2maf issue in that it is giving the NCBI_Build as GRCh37 even though the reference provided on the command line was GRCh38 and the input VCF doesn't list a reference.

field position	field name	values
1	Hugo_Symbol	'Unknown'
2	Entrez_Gene_Id	'0'
3	Center	'.'
4	NCBI_Build	'GRCh37'
5	Chromosome	chrs
6	Start_Position	[0-9]+
7	End_Position	[0-9]+ (= start)
8	Strand	'+'
9	Variant_Classification	'Targeted_Region'
10	Variant_Type	'SNP'
11	Reference_Allele	[ACGT]
12	Tumor_Seq_Allele1	[ACGT]
13	Tumor_Seq_Allele2	[ACGT]
16	Tumor_Sample_Barcode	'CPCG0000000196-T001-P01-F'
17	Matched_Norm_Sample_Barcode	'CPCG0196-B1'
18	Match_Norm_Seq_Allele1	[ACGT]
19	Match_Norm_Seq_Allele2	[ACGT]
40	t_depth	[0-9]+
41	t_ref_count	[0-9]+
42	t_alt_count	[0-9]+
43	n_depth	[0-9]+
44	n_ref_count	[0-9]+
45	n_alt_count	[0-9]+
109	FILTER	'PASS'
110	flanking_bps	[ACGT]{3}
111	vcf_id	'.'
112	vcf_qual	'.'
133	vcf_pos	[0-9]+ (= start)