GNU General Public License, GPLv3GNU General Public License, GPLv3
Variant annotation is a critical step in genomic data analysis, facilitating the interpretation of genetic variations and their potential biological significance. As large-scale whole-genome sequencing studies continue to expand, efficient storage, retrieval, and manipulation of variant annotation data have become increasingly important. The Genomic Data Structure (GDS) file format offers a scalable and storage-efficient solution for large genomic datasets, enabling rapid access and computational efficiency.
GDSAnnotator is an R package designed for fast and memory-efficient annotation of variants stored in GDS files. It integrates seamlessly into Bioconductor tools, and utilizes external data resources, e.g., Ensembl Variant Effect Predictor (VEP), SnpEff, gnomAD and FAVOR (Functional Annotation of Variants Online Resource), to provide comprehensive functional annotations, including predicted variant effects and functional characteristics of non-coding variants. Compared to a plain text file, GDS format is 30-40 times more space-efficient when storing whole-genome annotations of FAVOR.
Storing variant annotations in a GDS file was introduced by FAVOR with the annotated GDS (aGDS) format, in which the FAVOR functional annotations of the variants of a study are added to the SeqArray GDS file holding the genotypes. GDSAnnotator generalizes this format to annotation GDS files of any source, with or without genotypes: a whole-genome annotation database (FAVOR, gnomAD, Ensembl VEP, SnpEff, ...) is kept as one GDS file per chromosome and queried by position and alleles, and the annotations of the variants of a study are written into its genotype GDS file; with the FAVOR annotations, this produces an aGDS file.
Coming soon (the package is being prepared for submission). Once it is available:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("GDSAnnotator")
| Function | Description |
|---|---|
| seqToGDS_FAVOR | Convert FAVOR CSV files to GDS |
| seqToGDS_gnomAD | Convert gnomAD VCF files to GDS |
| seqToGDS_VEP | Convert Ensembl VEP VCF output to GDS |
| seqToGDS_SnpEff | Convert SnpEff VCF output to GDS |
| seqAnnotate | Annotate variants using the annotation stored in GDS |
| seqAnnotateVCF | Annotate the variants of a VCF file |
| seqAnnotateGDS | Annotate the variants of a SeqArray GDS file |
| seqAnnotList | List the annotations stored in the GDS file |
| seqValueCounts | Calculate the counts of unique values |
| seqAnnotStat | Calculate the summary statistics of variants and annotations |
| seqAnnotReport | Generate a summary report in HTML, Markdown or R Markdown format |
| seqAnnotGeneTable | Per-gene annotation counts, broken down by impact |
library(GDSAnnotator)
# FAVOR essential dataset of chromosome 22 (subset)
annot_gds <- system.file("extdata", "favor_chr22_sub.gds", package="GDSAnnotator")
# list the annotations in the gds file (return a DataFrame)
(ann <- seqAnnotList(annot_gds))
## DataFrame with 30 rows and 4 columns
## name type trait description
## <character> <factor> <character> <character>
## 1 apc_conservation Real Float32 NA
## 2 apc_conservation_v2 Real Float32 NA
## 3 apc_epigenetics Real Float32 NA
## 4 apc_epigenetics_active Real Float32 NA
## 5 apc_epigenetics_repr.. Real Float32 NA
## ... ... ... ... ...
## 26 genecode_comprehensi.. Logical Int32 NA
## 27 genehancer Logical Int32 NA
## 28 linsight Real Float32 NA
## 29 cadd_phred Real Float32 NA
## 30 rdhs Logical Int32 NA
varnm <- ann$name # use all annotation
snp <- c("22-10510007-T-C", "22-10510038-T-C", "22-10510282-G-C",
"22-10510303-G-C" # a fake SNP, return NA
) # a list of variants
seqAnnotate(snp, annot_gds, varnm)
## Open ‘favor_chr22_sub.gds’ [1,000 variants]
## [favor_chr22_sub.gds] # of variants found: 3
## [30] ..............................
## DataFrame with 4 rows and 30 columns
## apc_conservation apc_conservation_v2 apc_epigenetics apc_epigenetics_active ...
## <numeric> <numeric> <numeric> <numeric>
## 1 2.583288 2.232373 0.0874126 0.226559
## 2 4.766045 4.498693 0.0750365 0.226559
## 3 0.393781 0.323713 0.1819110 0.226559
## 4 NA NA NA NA
## ......