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Welcome to the plotVCF wiki! ...work-in-progress...

This wiki is intended to give you a more detailed explanation of plotVCF usage options and capacities than what is provided in the main GitHub page.

This wiki is divided accordingly to software main sections:

1. Installation and Requirements

• 1.1. Installation dependencies
• 1.2. Install plotVCF
• 1.3. plotVCF dependencies
• 1.4. VCF input file
• 1.5. RAM capacity
• 1.6. FASTA file

2. How to run plotVCF in your R session

• 2.1 load plotVCF

3. Main plotVCF functions:

• 3.1. Manhattan-style plots generation: visualize variants in your VCF file. Multiple plot options: position, sample, gene and/or exon, etc.
  • 3.1.1 basic visualization plot
  • 3.1.2 order
  • 3.1.3 user-defined VCF flag
  • 3.1.4 chromosome lines
  • 3.1.5 threshold
  • 3.1.6 Y-axis
  • 3.1.7 position
  • 3.1.8 samples
  • 3.1.9 single sample
  • 3.1.10 grouped
  • 3.1.11 gene
  • 3.1.12 exon
• 3.2. Chromosome summary plots generation
• 3.3. Gene summary plots generation

4. Save generated plots