VCF

 This document describes the VCF file format that GenomeJack supports.
Reference URL:
Note:
  1. VCF file is generated by mpileup command of samtools in the method described in the reference URL.
  2. VCF file shows the state of mutations. For example, if GA mutates into G, deletion is displayed instead of A. No mutation is displayed at first G.
  3. These files are added into Show table views.
  4. SNP is displayed in mutated base whose color is set as [Base Color] in Configure Preferences dialog. The kind of base except A, T, G and C is displayed in black.
  5. Deletion is displayed in black type H.
  6. Insertion is displayed in blue type I. Consecutive some insertions are displayed as one.
  7. The mutation except SNP, deletion and insertion is displayed in black square.
Restriction:
  1. The data lines must be sorted by the chromosome.
  2. The data from 1 sample is available.
  3. FORMAT data and sample data must correspond.