VPA (Variant Pattern Analyzer) is a package for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. To install VPA package in Unix-like operation system, the version of R should be >= 2.12.1. To install VPA package in Windows operation system, the version of R should be >=2.14.0.
|Date of publication||2013-08-30 20:22:11|
|Maintainer||Qiang Hu <email@example.com>|
filterpos: Filter variants against known SNP dataset
filtervcf: Filter variants with user-specified quality criteria
gefreq: Frequency analysis at gene level
getref: Download reference gene annotation
LoadFiltering: To load and filter variants in batch mode
Patterning: Extract variants with user-specified variant pattern
Pos2Gene: Map sequencing variants to gene
pos2seq: Positions to sequencing calls
read.vcf: Read VCF file
subvcf: Subset of VCF data
vcfreq: Variant frequency of a varlist
VPA-package: Extract variants from VCF data with specified variant...
write.vcf: Write VCF object