Biologists receive so much biological data that they have to spend a lot of time cleaning it up in order to get just the data they are interested in. HPG VCF Tools is a set of tools for preprocessing, filtering and manipulating VCF files. It aims to avoid excessive time consumption in tedious preprocessing tasks.

Current features

Split VCF

  • Chromosome

Filter VCF

  • By regions
  • By positions corresponding to a SNP
  • By a minimum quality
  • By a minimum coverage
  • By number of alleles

VCF stats

General stats

  • Number of variants
  • Number of samples
  • Number of bi-allelic sites
  • Number of multi-allelic sites
  • Number of SNP
  • Number of indels
  • Number of transitions
  • Number of transversions
  • Ti/TV ratio
  • Percentage of PASS
  • Average quality in the VCF

Statistics by variant

  • Allelic and genotypic counts and frequencies per variant
  • Number of missing alleles and genotypes

Feature plan

Split, filter and statistics tools will be enriched with more options. A merge tool will be included in the short-term. For more information, see the detailed feature plan.

User's manual

The user's manual is under development.


Current and previous releases are available at the following link:

Other tools suites