vcfR documentation
by
Brian J. Knaus and Niklaus J. Grünwald
Software that produce VCF files
A fun part of this project has been learning about how people use
vcfR. One facet of this is learning about the software that create VCF
files. So I’ve decided to make a list of these software. If you know of
a software that I have not included on this list, particularly if you
can report that vcfR works with its files, feel free to let me know!
Genomic variant callers
Restriction site associated DNA markers (e.g., RADseq,
GBS)
Manipulation of VCF data
- Beagle
v4.1 Inputs VCF genotypes and outputs phased genotypes to VCF
format
- Goby is a
next-gen data management framework designed to facilitate the
implementation of efficient data analysis pipelines.
- pegas::read.vcf
Population and Evolutionary Genetics Analysis System
- PyVCF
- SnpEff Genetic variant
annotation and effect prediction toolbox
- Picard A
set of command line tools (in Java) for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF
- VariantAnnotation::readVcf
Bioconductor package for annotating variants
- VCF-kit VCF-kit
is a command-line based collection of utilities for performing analysis
on Variant Call Format (VCF) files.
- VCFtools General
manipulation and analysis
- VEP
Variant Effect Predictor
R packages that read VCF data
Other VCF software
Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.
USDA Agricultural Research Service, Horticultural Crops Research Lab.