gcuellarpartida/vcf-annotator

VCF-annotator

Simple tool to annotate a VCF. This tool will create a csv file with annotations for variants in the VCF, including their type, position (coding, intergenic, etc) as well as annotations from ExAC (consequence, allele frequency, SIFT and polyphen). Sample information is also included.

Usage example

In R:

source("./vcf-annotation.R")
anno<-annotateVCF("challange.vcf")
#Sat Jan 30 16:02:47 2021: Reading VCF file challange.vcf...
#Sat Jan 30 16:02:48 2021: Read 6977 variants for 2 samples...
#Sat Jan 30 16:02:48 2021: Getting variants location relative to genes....
#Sat Jan 30 16:03:25 2021: Getting annotations for 3262 coding variants from ExAC...
#Sat Jan 30 16:03:40 2021: Generating .csv...
write.table(anno, file="annotated_vcf.tsv", quote=F, row.names=F, col.names=T, sep="\t")

Try the live REST API at https://genoma.io:

curl -v -F [email protected] http://tools.genoma.io/annotate-vcf >annotated_vcf.tsv

Launch your own REST API:

library(plumber)
r<-plumb("api.R")
r$run(port=8888)

Test it:

curl -v -F [email protected] http://localhost:8888/annotate-vcf >annotated_vcf.tsv

Output

The resuts .tsv file contains the following tab separated columns:

Column	Description
ExAC_id	variant name in ExAC friendly format (chr-position-ref-alt)
seqnames	seqname (chromosome)
start	variants start position
REF	reference allele
ALT	alternate allele
sample_AO	alternate allele observations
sample_RO	reference allele observations
sample_AOP	percentage of alternate allele observations vs reference
sample_DP	sequence depth
loc	location of variant relative to genes
exac_allele_freq	allele frequency reported by ExAC
exac_consequences	variant consequences reported by ExAC separated by semilocon in the following format: GeneID|Symbol|Consequence|rsID|PolyPhen

Dependencies

This has been tested in [R 4.0.3] and requires the following libraries:

• plumber (1.0.0)
• readr (1.4.0)
• jsonlite (1.6.0)
• httr (1.4.1)
• VariantAnnotation (1.36.0)
• TxDb.Hsapiens.UCSC.hg19.knownGene (3.2.0)

In R:

 install.packages("plumber")
 install.packages("jsonlite")
  install.packages("readr")
 install.packages("httr")
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 BiocManager::install("VariantAnnotation")
 BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
 BiocManager::install('snpStats')