| Environment | Status |
|---|---|
| BioC-release |  |
| BioC-devel |  |
The alabaster.vcf package implements methods for saving and loading VCF objects (from the VariantAnnotation package) under the alabaster framework.
It does so by converting them back into VCF files but with additional metadata to store the number of samples and positions.
To get started, install the package and its dependencies from Bioconductor:
# install.packages("BiocManager")
BiocManager::install("alabaster.vcf")In the example below, we save a VCF object to file:
library(VariantAnnotation)
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, genome="hg19")
vcf
## class: CollapsedVCF
## dim: 7 1
## rowRanges(vcf):
## GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
## info(vcf):
## DataFrame with 10 columns: BKPTID, CIEND, CIPOS, END, HOMLEN, HOMSEQ, IMPR...
## info(header(vcf)):
## Number Type Description
## BKPTID . String ID of the assembled alternate allele in the asse...
## CIEND 2 Integer Confidence interval around END for imprecise var...
## CIPOS 2 Integer Confidence interval around POS for imprecise var...
## END 1 Integer End position of the variant described in this re...
## HOMLEN . Integer Length of base pair identical micro-homology at ...
## HOMSEQ . String Sequence of base pair identical micro-homology a...
## IMPRECISE 0 Flag Imprecise structural variation
## MEINFO 4 String Mobile element info of the form NAME,START,END,P...
## SVLEN . Integer Difference in length between REF and ALT alleles
## SVTYPE 1 String Type of structural variant
## geno(vcf):
## List of length 4: GT, GQ, CN, CNQ
## geno(header(vcf)):
## Number Type Description
## GT 1 String Genotype
## GQ 1 Float Genotype quality
## CN 1 Integer Copy number genotype for imprecise events
## CNQ 1 Float Copy number genotype quality for imprecise events
library(alabaster.vcf)
tmp <- tempfile()
saveObject(vcf, tmp)
roundtrip <- readObject(tmp)
class(roundtrip)
## [1] "CollapsedVCF"
## attr(,"package")
## [1] "VariantAnnotation"