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.
- By regions
- By positions corresponding to a SNP
- By a minimum quality
- By a minimum coverage
- By number of alleles
- 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
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.
The user's manual is under development.
Current and previous releases are available at the following link: http://docs.bioinfo.cipf.es/projects/hpg-vcf/files