Table 1. SomaticSniper output file columns.

A description of each column of SomaticSniper’s output file is below.

Column #	Description
1	Chromosome name
2	Chromosomal location (1-based)
3	Reference base at this position
4	Genotype of tumor (as IUB code)
5	Genotype of normal (as IUB code)
6	Somatic Score
7	Tumor consensus quality
8	Tumor variant allele quality
9	Tumor mean mapping quality
10	Normal consensus quality
11	Normal variant allele quality
12	Normal mean mapping quality
13	Depth in tumor
14	Depth in normal
15	Mean base quality of reads supporting reference in tumor
16	Mean mapping quality of reads supporting reference in tumor
17	Depth of reads supporting reference in tumor
18	Mean base quality of reads supporting variant(s) in tumor
19	Mean mapping quality of reads supporting variant(s) in tumor
20	Depth of reads supporting variant(s) in tumor
21	Mean base quality of reads supporting reference in normal
22	Mean mapping quality of reads supporting reference in normal
23	Depth of reads supporting reference in normal
24	Mean base quality of reads supporting variant(s) in normal
25	Mean mapping quality of reads supporting variant(s) in normal
26	Depth of reads supporting variant(s) in normal